org.biopax.paxtools.model.level3
Interface BiochemicalPathwayStep

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level3Element, Observable, PathwayStep, java.io.Serializable, UtilityClass

All Known Implementing Classes:

BiochemicalPathwayStepImpl

public interface BiochemicalPathwayStep
extends PathwayStep

Definition: Imposes ordering on a step in a biochemical pathway.

Retionale: A biochemical reaction can be reversible by itself, but can be physiologically directed in the context of a pathway, for instance due to flux of reactants and products.

Usage: Only one conversion interaction can be ordered at a time, but multiple catalysis or modulation instances can be part of one step.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Conversion	getStepConversion() This method returns the central conversion of this BiochemicalPathwayStep.
StepDirection	getStepDirection() This property can be used for annotating direction of enzymatic activity.
void	setStepConversion(Conversion stepConversion) This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion.
void	setStepDirection(StepDirection stepDirection) This property can be used for annotating direction of enzymatic activity.

Methods inherited from interface org.biopax.paxtools.model.level3.PathwayStep

addNextStep, addStepProcess, getNextStep, getNextStepOf, getPathwayOrderOf, getStepProcess, removeNextStep, removeStepProcess

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Method Detail

getStepConversion

Conversion getStepConversion()

This method returns the central conversion of this BiochemicalPathwayStep. The returned conversion is also stepProcess of this PathwayStep. The step direction defines the direction of this conversion. The conversion must be reversible.

Returns:

The central conversion that take place at this step of the biochemical pathway.

setStepConversion

void setStepConversion(Conversion stepConversion)

This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion. Old step conversion is also removed from the stepProcess list.

getStepDirection

StepDirection getStepDirection()

This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.

Returns:

Direction of the conversion in this particular pathway context.

setStepDirection

void setStepDirection(StepDirection stepDirection)

This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.

Parameters:

stepDirection - Direction of the conversion in this particular pathway context.