package affectors;

import main.Node;
import main.Globals;

/** Use this for decay of a Node when the decay rate can be raised (half life lowered) by
the presence of another node.  Use this for both intracellular and extracellular nodes. 

<p> <b>Formula</b>
<br>dnodex/dt = -nodex * (1 / [H_nodex - (H_nodex - min_life) * (DECAYER^nu / (K^nu + DECAYER^nu))])

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Target [nodex]</td><td> The Node which is decaying</td></tr>
<tr><td>Inhibitor [DECAYER]</td><td> The Node that increases decay.</td></tr>
<tr><td>Half-life [H_nodex]</td><td> The half-life of the Node absent the decayer.</td></tr>
<tr><td>Half-max decayer [K_DECAYERnodex]</td><td> The decayer concentration at which decay rate is increased by half maximum increase.</td></tr>
<tr><td>Cooperativity decayer [nu_DECAYERnodex]</td><td> The non-linearity of the decayer function.</td></tr>
(tr><td>Min half-life [min_life]</td><td> The minimum half life reached when decayer is at max concentration.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&nodex
<blockquote>    &DecayRegUpAff  nodex  decayer	H_nodex	K_decayer_nodex	nu_decayer_nodex	min_life
</blockquote>
&endnodex</code></font>
*/
public class DecayRegUpAff extends Affector {
	/** The half-life of the Node in minutes. */
	int		halfLife, kParam, nuParam, minHalfLifeParam;

	static final String		desc = "First-order decay with up-regulation";
	static final String	[]	nodeDescriptions = {"Target", "Inhibitor"};
	static final String	[]	paramDescriptions = {"Half-life",
												"Kappa: Half-maximal level of inhibitor", 
												"nu: cooperativity of inhibitor",
												"min half-life"};
	static final int	[]	whichSides = { -1, -1 };

	public DecayRegUpAff()	{}

	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.HH;
		this.Type[TERMTYPE] = Affector.DEGRADATION;
	}
	
	public void setParameterNumbers(int [] param_nums)
	{
		halfLife = param_nums[0];
		kParam = param_nums[1];
		nuParam = param_nums[2];
		minHalfLifeParam = param_nums[3];
	}
	
	public float getValue(Node which_node)	{
		float	temp = (params[halfLife] - params[minHalfLifeParam]) * 
						Phi(Nodes[1].getIntegrationValue(), params[kParam], params[nuParam]);
		float	half_life = params[halfLife] - temp;
		return (Nodes[0].getIntegrationValue(side) * 
				(-Globals.characteristicTime / half_life));
	}

	public float getNCValue(Node which_node)  {
		float	temp = (params[halfLife] - params[minHalfLifeParam]) * 
						Phi(Nodes[1].getIntegrationValue(), params[kParam], params[nuParam]);
		float	half_life = params[halfLife] - temp;
		return (-Globals.characteristicTime / half_life);
	}
	
}