EnhancerRegionAff

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

affectors
Class EnhancerRegionAff

java.lang.Object
  affectors.Affector
      affectors.EnhancerRegionAff

All Implemented Interfaces:: java.lang.Cloneable

Direct Known Subclasses:: MultiEnhancerAff, Product, ProductAff, SaturationEnhancerAff, SumAff

public class EnhancerRegionAff
extends Affector

EnhancerRegion surrounds other enhancers and multiplies them by the scaling (characteristicTime / halfLife). This scaling needs to be used outside of all transcription terms once. When transcriptional terms are nested, as with Sum, Product, or MultiEnhancer, then they often can't include the scaling within the transcription term itself since it might be nested inside another term. So EnhancerRegion is used as an outside wrapper. EnhancerRegionAff will only wrap a single other affector, which will usually be either a MultiEnhancer or Product.

In some cases, you may not need to wrap other meta-affectors inside of this one. For instance, ProductAff can be used to multiply one of the standard transcription affectors times inhibitory terms. Since the standard transcription affectors already contain the proper scaling, that combination needs no further wrapping. For this all to become clear, you will probably need to work through the math yourself a bit, but as a rule of thumb, if you are using TxnSiteActivator or MultiEnhancer within your enhancer term, you need to wrap the whole term with an EnhancerRegion.

Note - this is also the base class for all other meta-affectors. If you make your own meta-affector, subclass it from EnhancerRegion.

Formula
dnodex/dt = (characteristicTime / H_nodex) * SubAffectorValue

Parameters

Half-life [H_nodex]

The half-life of the target mRNA

Usage &nodex

&EnhancerRegionAff nodex H_nodex &MultiEnhancerAff [in here are some other affectors] &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
`EnhancerRegionAff()`

Method Summary
`void`	`addAffector(Affector aff)` This function is used to add regular affectors to be used by the meta-affector.
`Affector`	`copy()`
`float`	`getNCValue(Node which_node)` Overrides Affector.getNCValue() to return the value of the wrapped enhancer multiplied by the scaling characteristicTime / halfLife
`Node[]`	`getNodes()` This function is here so that viewers can examine an affector.
`Affector`	`getSubaffector(int num)`
`float`	`getValue(Node which_node)` Overrides Affector.getValue() to return the value of the wrapped enhancer multiplied by the scaling characteristicTime / halfLife
`protected void`	`setLabelsAndTypes()` half life param
`void`	`setParameterNumbers(int[] param_nums)`
`void`	`setSide(int side)`

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