package affectors;

import main.Node;
import main.Globals;

/** This is one half of an affector that phosphorylates a single node.  Use this
affector in the unphosphorylated species.  Use the B version in the product species.
For either membrane-bound or cytoplasmic kinases, as long as target is cytoplasmic.

<p> <b>Formula</b>
<br>dSUBSTRATE/dt = -Pmax * SUBSTRATE * (KINASE^nu / (K_KINASE^nu + KINASE^nu))

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Substrate [SUBSTRATE]</td><td> The unphosphorylated Node </td></tr>
<tr><td> Kinase [KINASE]</td><td> The kinase Node.</td></tr>
<tr><td> Half-max activation [K_KINASE_SUBSTRATE]</td><td> The concentration of kinase at which it phosphorylates at half its maximum rate.</td></tr>
<tr><td> Cooperativity [nu_KINASE_SUBSTRATE]</td><td> The non-linearity in kinase activity as kinase concentration increases.</td></tr>
<tr><td> Max reaction rate [P_KINASE]</td><td> The maximum reaction rate.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&SUBSTRATE
<blockquote>    &PhosphorylationA_ICAff  SUBSTRATE	KINASE	K_KINASE_SUBSTRATE	nu_KINASE_SUBSTRATE	P_KINASE
</blockquote>
&endSUBSTRATE</code></font>

<p>@see PhosphorylationB_ICAff
<br>@see DephosphorylationB_ICAff
*/
public class PhosphorylationA_ICAff extends Affector {
	/** The level of kinase at which phosphrylation proceeds half-maximally. */
	int		kappaParam;
	/** The "cooperativity" exponent for the reaction. */
	int		nuParam;
	/** The maximal reaction rate. */
	int		pMaxParam;
	
	static final String		desc = "Intracellular phosphorylation of a substrate; version A for substrate";
	static final String	[]	nodeDescriptions = {"Unphosphorylated substrate", "Kinase"};
	static final String	[]	paramDescriptions = {"Kappa: half-maximal activity of the phosphatase",
										"nu: cooperativity of reaction",
										"Pmax: maximal reaction rate"};
	static final int	[]	whichSides = {-1, -1};
	
	public PhosphorylationA_ICAff()	{}
	
	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, nodeDescriptions, paramDescriptions);
		setSided(true, whichSides);
		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)
	{
		kappaParam = param_nums[0];
		nuParam = param_nums[1];
		pMaxParam = param_nums[2];
	}

	public float getValue(Node which_node)	{
		float total_kinase = Nodes[1].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm = params[pMaxParam] * source *
					Phi(total_kinase, params[kappaParam], params[nuParam]);

		return -Globals.characteristicTime * theTerm;
	}
	
	public float getNCValue(Node which_node)  {
		float total_kinase = Nodes[1].getIntegrationValue();
		float theTerm = params[pMaxParam] *
					Phi(total_kinase, params[kappaParam], params[nuParam]);

		return -Globals.characteristicTime * theTerm;
	}
}