org.biopax.paxtools.impl.level3

Class BiochemicalPathwayStepImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.PathwayStepImpl

org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, BiochemicalPathwayStep, Level3Element, Observable, PathwayStep, UtilityClass

public class BiochemicalPathwayStepImpl
extends PathwayStepImpl
implements BiochemicalPathwayStep

See Also:

Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
BiochemicalPathwayStepImpl()

Method Summary

Modifier and Type	Method and Description
void	addStepProcess(Process process)
Class<? extends BiochemicalPathwayStep>	getModelInterface() This method returns the actual model interface that a class implements.
Conversion	getStepConversion() This method returns the central conversion of this BiochemicalPathwayStep.
StepDirection	getStepDirection() This property can be used for annotating direction of enzymatic activity.
Set<Process>	getStepProcess()
void	setStepConversion(Conversion highLander) This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion.
void	setStepDirection(StepDirection newSTEP_DIRECTION) This property can be used for annotating direction of enzymatic activity.

Methods inherited from class org.biopax.paxtools.impl.level3.PathwayStepImpl

addEvidence, addNextStep, getEvidence, getNextStep, getNextStepOf, getPathwayOrderOf, removeEvidence, removeNextStep, removeStepProcess, setPathwayOrderOf

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, equivalenceCode, getAnnotations, getUri, hashCode, isEquivalent, semanticallyEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

addNextStep, getNextStep, getNextStepOf, getPathwayOrderOf, removeNextStep, removeStepProcess

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

addEvidence, getEvidence, removeEvidence

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

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getUri, isEquivalent

Constructor Detail

BiochemicalPathwayStepImpl

public BiochemicalPathwayStepImpl()

Method Detail

getModelInterface

public Class<? extends BiochemicalPathwayStep> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class PathwayStepImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getStepConversion

public Conversion getStepConversion()

Description copied from interface: BiochemicalPathwayStep

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.

Specified by:

getStepConversion in interface BiochemicalPathwayStep

Returns:

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

setStepConversion

public void setStepConversion(Conversion highLander)

Description copied from interface: BiochemicalPathwayStep

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

Specified by:

setStepConversion in interface BiochemicalPathwayStep

Parameters:

highLander - the Conversion interaction of this biological pathway step

addStepProcess

public void addStepProcess(Process process)

Specified by:

addStepProcess in interface PathwayStep

Overrides:

addStepProcess in class PathwayStepImpl

getStepDirection

public StepDirection getStepDirection()

Description copied from interface: BiochemicalPathwayStep

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.

Specified by:

getStepDirection in interface BiochemicalPathwayStep

Returns:

Direction of the conversion in this particular pathway context.

setStepDirection

public void setStepDirection(StepDirection newSTEP_DIRECTION)

Description copied from interface: BiochemicalPathwayStep

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.

Specified by:

setStepDirection in interface BiochemicalPathwayStep

Parameters:

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

getStepProcess

public Set<Process> getStepProcess()

Specified by:

getStepProcess in interface PathwayStep

Overrides:

getStepProcess in class PathwayStepImpl