import org.sbml.libsbml.*;

/**
 * @file answer_2.java
 * @brief Solution to tutorial example exercise 2
 * @author Sarah Keating
 * @author Frank Bergmann (java port)
 */

public class answer_2 {

	public static void main(String[] args) {

		System.loadLibrary("sbmlj");

		SBMLDocument d = new SBMLDocument(3, 1);

		Model m = d.createModel();

		// create the parameters
		Parameter p1 = m.createParameter();
		p1.setId("p1");
		p1.setUnits("metre");
		p1.setConstant(true);

		Parameter p2 = m.createParameter();
		p2.setId("p2");
		p2.setUnits("metre");
		p2.setConstant(true);

		Parameter p3 = m.createParameter();
		p3.setId("p3");
		p3.setUnits("metre_sq");
		p3.setConstant(false);

		Parameter p4 = m.createParameter();
		p4.setId("p4");
		p4.setUnits("metre_sq_per_sec");
		p4.setConstant(false);

		// value of p2 is assigned by initialAssignment

		InitialAssignment ia = m.createInitialAssignment();
		ia.setSymbol("p2");
		ia.setMath(libsbml.parseFormula("3*p1"));

		// value of p3 is by assignment rule

		AssignmentRule ar = m.createAssignmentRule();
		ar.setVariable("p3");
		ar.setMath(libsbml.parseFormula("p1*p2"));

		// p4 is a rate rule

		RateRule rr = m.createRateRule();
		rr.setVariable("p4");

		ASTNode time = new ASTNode(libsbml.AST_NAME_TIME);
		time.setName("t");
		ASTNode ast = libsbml.parseFormula("p3");
		ASTNode divide = new ASTNode(libsbml.AST_DIVIDE);
		divide.addChild(ast);
		divide.addChild(time);

		rr.setMath(divide);

		// now put in unit definitions for the units I used
		UnitDefinition ud1 = m.createUnitDefinition();
		ud1.setId("metre_sq");
		Unit u = ud1.createUnit();
		u.setKind(libsbml.UNIT_KIND_METRE);
		u.setExponent(2);
		u.setScale(0);
		u.setMultiplier(1);

		UnitDefinition ud2 = m.createUnitDefinition();
		ud2.setId("metre_sq_per_sec");
		Unit u1 = ud2.createUnit();
		u1.setKind(libsbml.UNIT_KIND_METRE);
		u1.setExponent(2);
		u1.setScale(0);
		u1.setMultiplier(1);
		Unit u2 = ud2.createUnit();
		u2.setKind(libsbml.UNIT_KIND_SECOND);
		u2.setExponent(-1);
		u2.setScale(0);
		u2.setMultiplier(1);

		libsbml.writeSBML(d, "Model_2.xml");

	}
}