package affectors;

import main.Globals;
import main.Node;

/** This is one third of a dimerization between a membrane bound and a cytoplasmic
protein, leading to a membrane bound complex.  Use this affector in the undimerized, membrane-
bound species.  Use the B version in the cytoplasmic undimerized species and the C version
in the dimer.  Be careful to put the membrane and cytoplasmic species in the right order
in the initializer.  The node_scale for each of the singleton proteins is the scaling
factor for the >other< singleton (i.e. in the membrane node, give cytoNode0 as node_scale
and vice-versa). The membrane bound Node will be taken from the membrane of the same cell
as the cytoplasmic Node.

<p> <b>Formula</b>
<br>dMEMBRANE_NODE/dt = - r * max_CYTO_NODE * MEMBRANE_NODE * CYTO_NODE

<p> <b>Parameters</b>
<table width="500" border="1">
<tr><td width="150">Membrane Node [MEMBRANE_NODE]</td><td> The undimerized Node that is on the membrane </td></tr>
<tr><td width="150">Cytoplasmic Node [CYTO_NODE]</td><td> The undimerized Node that is in the cytoplasm </td></tr>
<tr><td>Dimerization rate [r_DIMER]</td><td> The rate of the dimerization reaction.</td></tr>
<tr><td>Maximum Cyto [max_CYTO]</td><td> The maximum relative concentration of the cytoplasmic Node.</td></tr>
</table>

<p> <b>Usage</b>
<code><font size = "3"><br>&NODEX
<blockquote>    &DimerizeCytoMem_CAff  MEMBRANE_NODE  CYTO_NODE	r_DIMER	max_CYTO
</blockquote>
&endNODEX</code></font>
*/
public class DimerizeCytoMem_AAff extends Affector {
	/** The rate of the dimerization reaction. */
	int			kParam;
	/** The scaling factor of the other undimerized node in this reaction (i.e. max for cytoplasmic node). */
	int			nodeScaleParam;

	static final String		desc = "Dimerize membrane-bound & cytoplasmic node; version A for membrane-bound node";
	static final String	[]	nodeDescriptions = {"Membrane-bound node", "Cytoplasmic node"};
	static final String	[]	paramDescriptions = {"Second-order rate constant",
										"Scale factor (max value) for cytoplasmic node"};
	static final int	[]	whichSides = {-1, -1};
	
	public DimerizeCytoMem_AAff()	{}
	
	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)
	{
		kParam = param_nums[0];
		nodeScaleParam = param_nums[1];
	}
	
	public float getValue(Node which_node) {
		return -Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[0].getIntegrationValue(side) * Nodes[1].getIntegrationValue();
	}
	
	public float getNCValue(Node which_node)  {
		return -Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[1].getIntegrationValue();
	}
}