protected void setVars() {
Vector<SBMLReaction> reactions = this.model.getReactions();
for (int i = 0; i < reactions.size(); i++) {
SBMLReaction reac = (SBMLReaction) (reactions.elementAt(i));
String varName =
Integer.toString((Integer) this.model.getReactionsIdPositionMap().get(reac.getId()));
// String varName = Integer.toString(reac.getId());
double lb = reac.getLowerBound();
double ub = reac.getUpperBound();
if (reac.getKnockout().equals(GraphicalInterfaceConstants.BOOLEAN_VALUES[1])) {
lb = 0;
ub = 0;
}
this.getSolver().setVar(varName, VarType.CONTINUOUS, lb, ub);
}
}
protected void setConstraints(Vector<SBMLReaction> reactions, ConType conType, double bValue) {
ArrayList<Map<Integer, Double>> sMatrix = this.model.getSMatrix();
ModelCompressor compressor = new ModelCompressor();
ArrayList<Double> lowerBounds = new ArrayList<Double>();
ArrayList<Double> upperBounds = new ArrayList<Double>();
for (SBMLReaction reac : reactions) {
boolean ko = reac.getKnockout().equals(GraphicalInterfaceConstants.BOOLEAN_VALUES[1]);
lowerBounds.add(ko ? 0.0 : reac.getLowerBound());
upperBounds.add(ko ? 0.0 : reac.getUpperBound());
}
compressor.setsMatrix(sMatrix);
compressor.setLowerBounds(lowerBounds);
compressor.setUpperBounds(upperBounds);
compressor.compressNet();
sMatrix = compressor.getsMatrix();
for (int i = 0; i < sMatrix.size(); i++) {
this.getSolver().addConstraint(sMatrix.get(i), conType, bValue);
}
}
