package affectors;

import main.Node;
import main.Globals;

/**
 * <p>This is one half of an affector that phosphorylates a single node based on a kinase
 * activity.  Use this affector in the phosphorylated species.  Use {@link PhosphorylateA_Aff}
 * in the source (unphosphorylated) species.  For cytoplasmic proteins.</p>
 *
 * <p> <b>Formula</b>
 * <br>dNODEp/dt = PMax * NODE Phi(KINASE,K_kinase,nu_kinase)
 *
 * <p> <b>Parameters</b>
 * <table width="500" border="1">
 * <tr><td width="150">Phosphorylated Node [NODEp]</td><td> The phosphorylated Node</td></tr>
 * <tr><td width="150">Node [NODE]</td><td> The unphosphorylated Node</td></tr>
 * <tr><td width="150">Kinase [KINASE]</td><td> The kinase Node</td></tr>
 * <tr><td>Pmax [Pmax]</td><td> Maximal rate of phosporylation.</td></tr>
 * <tr><td>k_kinase [K_Kinase]</td><td> Concentration of kinase where activity is half maximal.</td></tr>
 * <tr><td>nu_kinase [nu_Kinase]</td><td> Apparent cooperativity of kinase activity.</td></tr>
 * </table>
 *
 * <p><b>Usage</b>
 * <code><font size = "3"><br>&Nodep
 * <blockquote>
 * 		&PhosphorylateB_Aff 	Node	Kinase	Pmax 	k_kinase 	nu_kinase
 * </blockquote>
 * &endNodep</code></font>
 *
 * @author Kerry Kim
 * @see PhosphorylateA_Aff
 */


public class PhosphorylateB_Aff extends Affector {
	int		pmax;
	int		k_kinase;
	int 	nu_kinase;
	static final String		affectorDescription = "Phosphorylation of cytoplasmic protein, use version B for phosphorylated";
	static final String	[]	nodeDescriptions = {"Protein to be phosphorylated", "Kinase"};
	static final String	[]	paramDescriptions = {"Maximal rate of phosphorylation",
												 "half maximal kinase concentration",
												 "Cooperativity of kinase"};

	static final int	[]	whichSides = { -1,-1 };

	public PhosphorylateB_Aff()	{}

	protected void setLabelsAndTypes()	{
		setDescriptions(affectorDescription, nodeDescriptions, paramDescriptions);
		setContainsTarget(true);

		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.GG;
		this.Type[TERMTYPE] = Affector.CONVERSION;
	}
	
	public void setParameterNumbers(int [] param_nums)
	{
		pmax = param_nums[0];
		k_kinase = param_nums[1];
		nu_kinase = param_nums[2];
	}
	
	public float getValue(Node which_node)	{
		float total_kinase = Nodes[1].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm = params[pmax] * source *
					Phi(total_kinase, params[k_kinase], params[nu_kinase]);

		return Globals.characteristicTime * theTerm;
	}
}