package affectors;

import main.Node;
import main.Globals;

/** This is one half of an affector that dephosphorylates a single node at a speed determined
by a phosphatase enzyme according to a sigmoid curve.  Use this
affector in the phosphorylated species.  Use the B version in the product species.
For either membrane-bound or cytoplasmic phosphatases, as long as target is cytoplasmic.

<p> <b>Formula</b>
<br>dSUBSTRATE_P/dt = -Pmax * SUBSTRATE_P * (PHOSPHO^nu / (K_PHOSPHO^nu + PHOSPHO^nu))

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Substrate [SUBSTRATE_P]</td><td> The unphosphorylated Node </td></tr>
<tr><td> Phosphotase [PHOSPHO]</td><td> The phosphatase Node.</td></tr>
<tr><td> Half-max activation [K_PHOSPHO_SUBSTRATE_P]</td><td> The concentration of phosphatase at which it de-phosphorylates at half its maximum rate.</td></tr>
<tr><td> Cooperativity [nu_PHOSPHO_SUBSTRATE_P]</td><td> The non-linearity in phosphatase activity as phosphatase concentration increases.</td></tr>
<tr><td> Max reaction rate [P_PHOSPHO]</td><td> The maximum reaction rate.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&SUBSTRATE_P
<blockquote>    &DephosphorylationA_ICAff  SUBSTRATE_P	PHOSPHO	K_PHOSPHO_SUBSTRATE_P	nu_PHOSPHO_SUBSTRATE_P	P_PHOSPHO
</blockquote>
&endSUBSTRATE_P</code></font>

@see DephosphorylationB_ICAff
@see PhosphorylationB_ICAff
*/
public class Dephosphor1StepA_ICAff extends Affector {
	/** The level of phosphatase at which the reaction proceeds half-maximally. */
	int		kappaParam;
	/** The "cooperativity" exponent for the reaction. */
	int		nuParam;
	/** The maximal reaction rate. */
	int		dMaxParam;
	
	static final String		desc = "Intracellular direct dephosphorylation of a substrate by a phosphatase; version A for substrate";
	static final String	[]	nodeDescriptions = {"Phosphorylated substrate", "Phosphatase"};
	static final String	[]	paramDescriptions  = {"Dmax: maximal reaction rate"};
	
	public Dephosphor1StepA_ICAff()	{}

	protected void setLabelsAndTypes()	{
		setDescriptions(this.desc, 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)
	{
		dMaxParam = param_nums[0];
	}

	public float getValue(Node which_node)	{
		float total_phosphatase = Nodes[1].getIntegrationValue();
		float source = Nodes[0].getIntegrationValue();
		float theTerm = params[dMaxParam] * source * total_phosphatase;

		return -Globals.characteristicTime * theTerm;
	}
	
	public float getNCValue(Node which_node)  {
		float total_phosphatase = Nodes[1].getIntegrationValue();
		float theTerm = params[dMaxParam] * total_phosphatase;

		return -Globals.characteristicTime * theTerm;
	}
}