affectors
Class MultiEnhancerAff

java.lang.Object
  affectors.Affector
      affectors.EnhancerRegionAff
          affectors.MultiEnhancerAff

All Implemented Interfaces:

java.lang.Cloneable

public class MultiEnhancerAff

extends EnhancerRegionAff

implements java.lang.Cloneable

This is a meta-affector which sums together transcriptional activation terms while keeping the total transcription rate less than or equal to 1. Each sub-affector is assumed to be giving a probability per some unit time of the transcription machinery binding to the promoter and starting transcription. MultiEnhancerAff figures out the total probability of the transcription machinery based on the individual probabilities.

Formula
dnodex/dt = 1 - (1 - alpha_T1/max_alpha * T1)(1 - alpha_T2/max_alpha * T2) ... (1 - alpha_Tn/max_alpha * Tn)
where T1 ... Tn are the sub-affector values and max_alpha is the max of all the alpha's

Parameters
There needs to be one alpha parameter per subaffector. The alphas give the relative weights of each subaffectors contribution to the total value.

Usage
&nodex

&EnhancerRegionAff

&MultiEnhancerAff alpha_AC alpha_SC

&TxnSiteActivatorAff AC K_ACsc nu_ACsc
&TxnSiteActivatorAff SC K_SCsc nu_SCsc

&endMultiEnhancerAff

&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

MultiEnhancerAff()

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

MultiEnhancerAff

public MultiEnhancerAff()

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