affectors
Class SaturationEnhancerAff

java.lang.Object
  affectors.Affector
      affectors.EnhancerRegionAff
          affectors.SaturationEnhancerAff

All Implemented Interfaces:

java.lang.Cloneable

public class SaturationEnhancerAff

extends EnhancerRegionAff

This is the wrapper for meta-affectors which need to be put through a saturating function. Use around Sum and Product Affectors when the terms inside of those don't saturate on their own. SaturationEnhancerAff can have only one affector inside of it, which will generally be either a ProductAff or SumAff. The sub-affector's value is put through a saturating S-shaped function, similar to the function in the regular transcription Affectors. If A is the value of the sub-affector than SaturatingEnhancerAff's value is:
A^nu / (K^nu + A^nu)
which is just the Phi function
SaturatingEnhancerAff should always be used inside of EnhancerRegionAff.

Formula
dnodex/dt = SubAffectorValue^nu / (K^nu + SubAffectorValue^nu)

Parameters

Half-max activation [K_nodex]	The value of the sub-affector at which the mRNA is transcribed at half its maximal rate.
Cooperativity [nu_nodex]	The non-linearity in transcription rates response to the sub-affectors value.

Usage
&nodex

&EnhancerRegionAff H_nodex

&SaturatingEnhancerAff nodex K_nodex nu_nodex

&SumAff

[in here are some other affectors]

&endSumAff

&endSaturatingEnhancerAff

&endEnhancerRegionAff

&endnodex

Field Summary

Fields inherited from class affectors.Affector

ADesc, affectorType, CC, CERTIFICATION, CONVERSION, copyNumber, DEGRADATION, FF, firstFreeParam, GG, GUI_CAPABLE, HH, KK, MATHTYPE, NDesc, PDesc, PRODUCTION, RETURNS_DERIV, RETURNS_PARTIALS, TERMTYPE, TT, Type, UNSPECIFIED

Constructor Summary

SaturationEnhancerAff()

Method Summary

Affector	copy()
float	getNCValue(Node which_node) Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.
float	getValue(Node which_node) Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.
protected void	setLabelsAndTypes() half life param
void	setParameterNumbers(int[] param_nums)

Methods inherited from class affectors.EnhancerRegionAff

addAffector, getNodes, getSubaffector, setSide

Methods inherited from class affectors.Affector

addDefaultParam, Chi, clearStatic, copy_, doesContainTarget, findOrCreateParam, findParam, fixNodes, getNumNodes, getNumParameters, getOtherSide, getParameter, getParameter, getParamName, getParamPos, getParamValue, getParamValue, getParamVariationMode, init, isLinearInTarget, Phi, Psi, setContainsTarget, setDescriptions, setParameter, setParamRange, setParamRange, setParamValue, setParamValue, setSided

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SaturationEnhancerAff

public SaturationEnhancerAff()

Method Detail

setLabelsAndTypes

protected void setLabelsAndTypes()

Description copied from class: EnhancerRegionAff

half life param

Overrides:

setLabelsAndTypes in class EnhancerRegionAff

setParameterNumbers

public void setParameterNumbers(int[] param_nums)

Overrides:

setParameterNumbers in class EnhancerRegionAff

getValue

public float getValue(Node which_node)

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

Overrides:

getValue in class EnhancerRegionAff

getNCValue

public float getNCValue(Node which_node)

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

Overrides:

getNCValue in class EnhancerRegionAff

copy

public Affector copy()

Overrides:

copy in class EnhancerRegionAff