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:

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

@Entity
@Indexed
public class BiochemicalPathwayStepImpl
extends PathwayStepImpl
implements BiochemicalPathwayStep

See Also:

Serialized Form

Nested Class Summary

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

BioPAXElement.Key

Field Summary

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

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

BiochemicalPathwayStepImpl()

Method Summary

java.lang.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.
void	setStepConversion(Conversion newSTEP_CONVERSION) 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, addStepProcess, getEvidence, getNextStep, getNextStepOf, getPathwayOrderOf, getStepProcess, removeEvidence, removeNextStep, removeStepProcess, setEvidence, setNextStep, setNextStepOf, setPathwayOrderOf, setStepProcess

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

addComment, getComment, removeComment, setComment

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

equivalenceCode, getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, semanticallyEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence

Constructor Detail

BiochemicalPathwayStepImpl

public BiochemicalPathwayStepImpl()

Method Detail

getModelInterface

public java.lang.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 newSTEP_CONVERSION)

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

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.