void species::resetToInitConc(acs_double tmpVolumeBeforeDivision, acs_double tmpVolume, bool tmpRndConcentration, acs_double tmpTheta, acs_int tmpStochDivision, MTRand& tmp_rndDoubleGen){
if(tmpTheta == 0) // IF division is not considered
{
concentration=firstConcentration;
concToNum(tmpVolume, tmp_rndDoubleGen);
if(tmpRndConcentration){amount = random_poisson(acs_double(amount),tmp_rndDoubleGen);}
numToConc(tmpVolume);
}else{
if(!concentrationFixed)
{
if (amount >= 1)
{
if(tmpStochDivision==1) // IF stochastic division
{
amount = random_poisson(acs_double(amount/(tmpVolumeBeforeDivision/tmpVolume)),tmp_rndDoubleGen);
numToConc(tmpVolume);
}else{
if(amount > 1){amount = acsround((acs_double)amount/(tmpVolumeBeforeDivision/tmpVolume),tmp_rndDoubleGen);}
else{if(tmp_rndDoubleGen() < (tmpVolume/tmpVolumeBeforeDivision)){amount = 1;}else{amount = 0;}}
numToConc(tmpVolume);
}
}else{
if(amount != 0){
ExitWithError("species::resetToInitConc","FATAl ERROR: The amount the molecules should be 0!!!");
}
}
}else{
concToNum(tmpVolume,tmp_rndDoubleGen);
}
}
}
static GnmValue *
gnumeric_randpoisson (GnmFuncEvalInfo *ei, GnmValue const * const *argv)
{
gnm_float x = value_get_as_float (argv[0]);
if (x < 0)
return value_new_error_NUM (ei->pos);
return value_new_float (random_poisson (x));
}
static gboolean
tool_random_engine_run_poisson (data_analysis_output_t *dao,
tools_data_random_t *info,
poisson_random_tool_t *param)
{
int i, n;
for (i = 0; i < info->n_vars; i++) {
for (n = 0; n < info->count; n++) {
gnm_float v;
v = random_poisson (param->lambda);
dao_set_cell_float (dao, i, n, v);
}
}
return FALSE;
}
/** \brief This constructor is used when a new species is uploaded from file (CONCENTRATION BASED). Currently we are using this one
@param tmpID species identificator
@param tmpSequence species sequence (e.g. ABABAABABA)
@param tmpAmount species initial amount of molecules
@param tmpReactions_constant ????
*/
species::species(acs_longInt tmpID, string tmpSequence, acs_double tmpConcentration, acs_double tmpDiffusionEnh,
acs_int tmpSoluble, acs_double tmpComplexDegEnh, acs_int tmpComplexCuttingPoint,
acs_int tmpEvalueted, acs_double tmpAge, acs_int tmpReborns, acs_double tmpVolume,
acs_longInt tmpNotUsedCatID, acs_longInt tmpNotUsedSubID, acs_double tmpK_phospho,
acs_double tmpKLoadConc, acs_int tmpLockConc, acs_double tmpInflux_rate, acs_int tmpMaxLOut,
bool tmpRndConcentration, acs_double tmpAlpha, MTRand& tmp_RndDoubleGen, int tmpSystemArchitecture)
{
cout << "\t|- CONCENTRATION BASED SPECIES CONSTRUCTOR FROM FILE -|\n";
id = tmpID;
sequence = tmpSequence;
chargedMols = round(tmpKLoadConc*tmpVolume*AVO);
age = tmpAge;
reborns = tmpReborns;
diffusionEnh =tmpDiffusionEnh;
soluble = tmpSoluble;
complexDegradationEnh = tmpComplexDegEnh;
complexCuttingPoint = tmpComplexCuttingPoint;
evaluated = tmpEvalueted;
catalyst_ID = tmpNotUsedCatID;
substrate_ID = tmpNotUsedSubID;
K_phospho = tmpK_phospho;
energizable = tmpLockConc;
// CONCENTRATION SETTINGS
//cout << "concentration based random concentration: " << tmpRndConcentration << endl;
//cin.ignore().get();
concentration = tmpConcentration;
concToNum(tmpVolume, tmp_RndDoubleGen);
if(tmpRndConcentration){amount = random_poisson(acs_double(amount),tmp_RndDoubleGen);}
numToConc(tmpVolume);
// Set concentrationFixed proprerty
// concentrationFixed = false;
// if((tmpInflux_rate == 0) && (tmpMaxLOut > 0)){ if(sequence.length() <= tmpMaxLOut) concentrationFixed = true;}
if (tmpSystemArchitecture == PROTOCELLFLUXBUFFERED)
{
if(tmpLockConc == 1) concentrationFixed = true;
else concentrationFixed = false;
}else{concentrationFixed = false;}
firstConcentration = tmpConcentration; // If the species is loaded from file that's the very initial concentration
lastSpeciesEvaluated = 0;
alpha = tmpAlpha;
}
/** \brief This constructor is used when a new species is uploaded from file (TOTAL AMOUNT BASED)
@param tmpID species identificator
@param tmpSequence species sequence (e.g. ABABAABABA)
@param tmpAmount species initial amount of molecules
@param tmpReactions_constant ????
*/
species::species(acs_longInt tmpID, string tmpSequence, acs_longInt tmpAmount, acs_double tmpDiffusionEnh,
acs_int tmpSoluble, acs_double tmpComplexDegEnh, acs_int tmpComplexCuttingPoint,
acs_int tmpEvalueted, acs_double tmpAge, acs_int tmpReborns, acs_double tmpVolume,
acs_longInt tmpNotUsedCatID, acs_longInt tmpNotUsedSubID, acs_double tmpK_phospho,
acs_int tmpEnergizable, acs_double tmpInflux_rate, acs_int tmpMaxLOut,
bool tmpRndConcentration, acs_double tmpAlpha, MTRand& tmp_RndDoubleGen)
{
id = tmpID;
sequence = tmpSequence;
amount = tmpAmount;
chargedMols = 0;
numToConc(tmpVolume); // The concetration is set within this function
age = tmpAge;
reborns = tmpReborns;
diffusionEnh =tmpDiffusionEnh;
soluble = tmpSoluble;
complexDegradationEnh = tmpComplexDegEnh;
complexCuttingPoint = tmpComplexCuttingPoint;
evaluated = tmpEvalueted;
catalyst_ID = tmpNotUsedCatID;
substrate_ID = tmpNotUsedSubID;
K_phospho = tmpK_phospho;
energizable = tmpEnergizable;
//cout << "concentration based random concentration: " << tmpRndConcentration << endl;
//cin.ignore().get();
if(tmpRndConcentration){amount = random_poisson(acs_double(amount),tmp_RndDoubleGen);}
numToConc(tmpVolume);
// Set concentrationFixed propriety
concentrationFixed = false;
if((tmpInflux_rate == 0) && (tmpMaxLOut > 0)){ if(sequence.length() <= tmpMaxLOut) concentrationFixed = true;}
firstConcentration = concentration; // If the species is loaded from file that's the very initial concentration
lastSpeciesEvaluated = 0;
alpha = tmpAlpha;
}
