package affectors;

import main.Node;
import main.Globals;

/**
 * TxnLeakyCyce implements leaky transcriptional activation under the control of two equivalent activators
 * and one inhibitor.  The activation is a sigmoidal curve based on the sum of the two activators.
 * The inhibitor is a noncompetetive inhibitor of transcription.  The activator and inhibitor are
 * cytoplasmic.  There is a basal rate of transcription which is not affected by the activator, but
 * which is inhibited by the repressor.  This is used for the transcription of cyce in the endocycle.
 * <p>
 * <b>Formula</b>
 * <br>dcyce/dt = 1/Hcyce (base+(1-base)(((ACT1+ACT2)/K_Act)^nu_Act/(1+(((ACT1+ACT2)/K_Act))^nu_Act+(INH/K_Inh)^nu_Inh))) Psi[INH, K_Inh, nu_Inh]
 * <p>
 * <b>Parameters</b>
 * <table width="500" border="1">
 * <tr><td width="150"> Half life of cyce [Hcyce] </td><td> Half life of cyce </td></tr>
 * <tr><td> Basal transcription rate [base] </td><td> The basal transcription rate of cyce in absence of activator </td></tr>
 * <tr><td> Activator 1 [ACT1] </td><td> The first activator node of cyce transcription </td></tr>
 * <tr><td> Activator 2 [ACT2] </td><td> The second activator node of cyce transcription </td></tr>
 * <tr><td> Inhibitor [INH] </td><td> The inhibitor node of cyce transcription </td></tr>
 * <tr><td> Half maximal activation level [K_Act] </td><td> The concentration of activator at which transcription proceeds at half its maximal rate </td></tr>
 * <tr><td> Half maximal inhibition level [K_Inh] </td><td> The concentration of inhibitor at which transcription is half of what it would be otherwise</td></tr>
 * <tr><td> Activation cooperativity [nu_Act] </td><td> The non-linearity of the activating function. The higher the value, the sharper the curves in the S-shaped activation function </td></tr>
 * <tr><td> Inhibition cooperativity [nu_Inh] </td><td> The non-linearity of the inhibition function. The higher the value, the sharper the curves in the S-shaped inhibition function </td></tr>
 * </table>
 * <p>
 * <b>Usage</b>
 * <code><font size = "3"><br>&cyce
 * <blockquote>
 * 		&TxnLeakyCyceAff   ACT1 ACT2 INH H_cyce base K_Act K_Inh nu_Act nu_Inh
 * </blockquote>
 * &endcyce</code></font>
 *
 * @author Kerry Kim
 */


public class TxnLeakyCyceAff extends Affector {
	/** Half life of RNA:*/
	int		h_cyce;
	/** base transcriptional rate */
	int		base;
	/** Half maximal activation concentration */
	int 	k_act;
	/** Half maximal inhibition concentration */
	int 	k_inh;
	/** Cooperativity of activation */
	int 	nu_act;
	/** Cooperativity of inhibition */
	int 	nu_inh;
	
	static final String		affectorDescription = "Leaky transcription activated by sum of 2 activators, 1 inhibitor";
	static final String	[]	nodeDescriptions = {"Activator 1","Activator 2","Inhibitor"};
	static final String	[]	paramDescriptions = {"Half life of RNA",
												 "Base transcription rate",
												 "Half maximal activation",
												 "Half maximal inhibition",
												 "Cooperativity of activation",
												 "Cooperativity of inhibition"};

	/* This list of integers specifies whether each Node used by the Affector is in the
		same cell as the Affectors Node, or is a neighboring cell. Put -1 for Nodes in
		the same cell, 1 for Nodes in neighboring cells. The numbers here correspond to
		the descriptions in nodeDescriptions above. */
	static final int	[]	whichSides = { -1,-1,-1};

	/* Constructor for this Affector. All Affectors must use a no-argument constructor, and
		currently there is no need to do anything in the constructor of most Affectors.
		You do need to change the name here from TemplateAff to [YourAffectorsName]Aff. */
	public TxnLeakyCyceAff()	{}

	/* Tells the rest of Ingeneue about this Affector. See the tutorial for the meaning
		of each line. */
	protected void setLabelsAndTypes()	{
		setDescriptions(affectorDescription, nodeDescriptions, paramDescriptions);
		this.Type[GUI_CAPABLE] = 1;
		this.Type[CERTIFICATION] = Affector.RETURNS_DERIV;
		this.Type[MATHTYPE] = Affector.FF;
		this.Type[TERMTYPE] = Affector.PRODUCTION;
	}
	
	/*  This is where the rest of Ingeneue gives this Affector indices to each parameter
		that it uses. You should  make a line for each parameter in the same order as
		they are described in paramDescriptions above, and then assign the values from param_nums
		as shown in the example below. */
	public void setParameterNumbers(int [] param_nums)
	{
		h_cyce 	= param_nums[0];
		base 	= param_nums[1];
		k_act 	= param_nums[2];
		k_inh 	= param_nums[3];
		nu_act 	= param_nums[4];
		nu_inh 	= param_nums[5];
	}
	
	/* This is the formula for this Affector.
		Use Nodes[a].getIntegrationValue(side) to get the value of a node, where a is
		the position of the node in the nodeDescriptions array (starting from 0).
		Use params[parameterIndex] to get the value of a parameter, where parameterIndex
		is the index value assigned in setParameterNumbers (for instance, firstParameter or
		secondParameter in the example above).
		Most Affectors should be multiplied by Globals.characteristicTime.
		This example is the formula for DecayAff. */
	public float getValue(Node which_node)	{
		float act = (Nodes[0].getIntegrationValue()+Nodes[1].getIntegrationValue())/params[k_act];
		act=(float)Math.pow((double)act,(double)params[nu_act]);
		float inh=Nodes[2].getIntegrationValue()/params[k_inh];
		inh=(float)Math.pow((double)inh,(double)params[nu_inh]);
		float noncomp=1-(inh/(1+inh));
		return (Globals.characteristicTime/params[h_cyce])*(params[base]+(1-params[base])*(act/(1+act+inh)))*noncomp;
	}
}