private void InitializeFromFbcV2(Model model, FbcModelPlugin plugin)
{
if (!plugin.getStrict())
{
Warnings.Add(
"Encountered non-strict model, this software does not support any of the dynamic features of FBC V2, only the static features of the model are imported. ");
}
var numConstraints = plugin.getNumFluxBounds();
for (int i = 0; i < numConstraints; i++)
{
var constraint = plugin.getFluxBound(i);
Constraints.Add(new LPsolveConstraint(constraint.getReaction(), GetOperator(constraint.getOperation()),
constraint.getValue()));
}
var activeObjective = plugin.getActiveObjective();
if (activeObjective == null && plugin.getNumObjectives() > 0)
activeObjective = plugin.getObjective(0);
if (activeObjective == null) return;
var numObjectives = (int)activeObjective.getNumFluxObjectives();
for (int i = 0; i < numObjectives; i++)
{
var objective = activeObjective.getFluxObjective(i);
Objectives.Add(new LPsolveObjective(objective.getReaction(), objective.getCoefficient()));
}
if (activeObjective.getType() == "minimize" || activeObjective.getType() == "minimise") Mode = FBA_Mode.minimize;
else Mode = FBA_Mode.maximize;
ActiveObjective = activeObjective.getId();
for (int i = 0; i < model.getNumReactions(); i++)
{
var reaction = model.getReaction(i);
ReversibilityMap[reaction.getId()] = reaction.getReversible();
var rplug = (FbcReactionPlugin) reaction.getPlugin("fbc");
if (rplug == null) continue;
if (rplug.isSetLowerFluxBound())
{
var param = model.getParameter(rplug.getLowerFluxBound());
if (param != null)
{
Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.GE,
param.getValue()));
}
}
if (rplug.isSetUpperFluxBound())
{
var param = model.getParameter(rplug.getUpperFluxBound());
if (param != null)
{
Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.LE,
param.getValue()));
}
}
}
}
private void InitializeFromFbcV1(Model model, FbcModelPlugin plugin)
{
var numConstraints = plugin.getNumFluxBounds();
for (int i = 0; i < numConstraints; i++)
{
var constraint = plugin.getFluxBound(i);
Constraints.Add(new LPsolveConstraint(constraint.getReaction(), GetOperator(constraint.getOperation()),
constraint.getValue()));
}
var activeObjective = plugin.getActiveObjective();
if (activeObjective == null && plugin.getNumObjectives() > 0)
activeObjective = plugin.getObjective(0);
if (activeObjective == null) return;
var numObjectives = (int)activeObjective.getNumFluxObjectives();
for (int i = 0; i < numObjectives; i++)
{
var objective = activeObjective.getFluxObjective(i);
Objectives.Add(new LPsolveObjective(objective.getReaction(), objective.getCoefficient()));
}
if (activeObjective.getType() == "minimize" || activeObjective.getType() == "minimise") Mode = FBA_Mode.minimize;
else Mode = FBA_Mode.maximize;
ActiveObjective = activeObjective.getId();
for (int i = 0; i < model.getNumReactions(); i++)
{
var reaction = model.getReaction(i);
ReversibilityMap[reaction.getId()] = reaction.getReversible();
}
}