org.biopax.paxtools.impl.level3

Class PathwayStepImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.PathwayStepImpl

All Implemented Interfaces:

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

Direct Known Subclasses:

BiochemicalPathwayStepImpl

@Entity
 @Indexed
public class PathwayStepImpl
extends L3ElementImpl
implements PathwayStep

See Also:

Serialized Form

Field Summary

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

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
PathwayStepImpl() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addEvidence(Evidence evidence)
void	addNextStep(PathwayStep nextStep)
void	addStepProcess(Process processStep)
Set<Evidence>	getEvidence()
Class<? extends PathwayStep>	getModelInterface() This method returns the actual model interface that a class implements.
Set<PathwayStep>	getNextStep()
Set<PathwayStep>	getNextStepOf()
Pathway	getPathwayOrderOf()
Set<Process>	getStepProcess()
void	removeEvidence(Evidence evidence)
void	removeNextStep(PathwayStep nextStep)
void	removeStepProcess(Process processStep)
void	setEvidence(Set<Evidence> evidence)
protected void	setNextStep(Set<PathwayStep> nextStep)
protected void	setNextStepOf(Set<PathwayStep> nextStepOf)
protected void	setPathwayOrderOf(Pathway pathwayOrderOf)

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

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

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

equals, equivalenceCode, getAnnotations, getPk, getRDFId, 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.Level3Element

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

PathwayStepImpl

public PathwayStepImpl()

Constructor.

Method Detail

getModelInterface

public Class<? extends PathwayStep> getModelInterface()

Description copied from interface: BioPAXElement

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

Specified by:

getModelInterface in interface BioPAXElement

Returns:

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

getNextStep

public Set<PathwayStep> getNextStep()

Specified by:

getNextStep in interface PathwayStep

addNextStep

public void addNextStep(PathwayStep nextStep)

Specified by:

addNextStep in interface PathwayStep

removeNextStep

public void removeNextStep(PathwayStep nextStep)

Specified by:

removeNextStep in interface PathwayStep

setNextStep

protected void setNextStep(Set<PathwayStep> nextStep)

getNextStepOf

public Set<PathwayStep> getNextStepOf()

Specified by:

getNextStepOf in interface PathwayStep

setNextStepOf

protected void setNextStepOf(Set<PathwayStep> nextStepOf)

getStepProcess

public Set<Process> getStepProcess()

Specified by:

getStepProcess in interface PathwayStep

addStepProcess

public void addStepProcess(Process processStep)

Specified by:

addStepProcess in interface PathwayStep

removeStepProcess

public void removeStepProcess(Process processStep)

Specified by:

removeStepProcess in interface PathwayStep

getEvidence

public Set<Evidence> getEvidence()

Specified by:

getEvidence in interface Observable

addEvidence

public void addEvidence(Evidence evidence)

Specified by:

addEvidence in interface Observable

removeEvidence

public void removeEvidence(Evidence evidence)

Specified by:

removeEvidence in interface Observable

setEvidence

public void setEvidence(Set<Evidence> evidence)

getPathwayOrderOf

public Pathway getPathwayOrderOf()

Specified by:

getPathwayOrderOf in interface PathwayStep

setPathwayOrderOf

protected void setPathwayOrderOf(Pathway pathwayOrderOf)