Package org.biopax.paxtools.impl.level3

Class SequenceSiteImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.SequenceLocationImpl

org.biopax.paxtools.impl.level3.SequenceSiteImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Level3Element, SequenceLocation, SequenceSite, UtilityClass

public class SequenceSiteImpl
extends SequenceLocationImpl
implements SequenceSite

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	Description
SequenceSiteImpl()

Method Summary

Modifier and Type	Method	Description
int	equivalenceCode()	If two elements are equivalent, then their equivalence code should be the same.
Class<? extends SequenceSite>	getModelInterface()	This method returns the actual model interface that a class implements.
PositionStatusType	getPositionStatus()
int	getSequencePosition()
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setPositionStatus(PositionStatusType positionStatus)
void	setSequencePosition(int sequencePosition)
String	toString()

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

addComment, getComment, removeComment, setComment

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

equals, getAnnotations, getUri, hashCode, isEquivalent

Methods inherited from class java.lang.Object

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

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

getAnnotations, getUri, isEquivalent

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

addComment, getComment, removeComment

Constructor Details

SequenceSiteImpl

public SequenceSiteImpl()

Method Details

getModelInterface

public Class<? extends SequenceSite> 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 SequenceLocationImpl

Returns:

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

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.

toString

public String toString()

Overrides:

toString in class BioPAXElementImpl

getPositionStatus

public PositionStatusType getPositionStatus()

Specified by:

getPositionStatus in interface SequenceSite

setPositionStatus

public void setPositionStatus(PositionStatusType positionStatus)

Specified by:

setPositionStatus in interface SequenceSite

getSequencePosition

public int getSequencePosition()

Specified by:

getSequencePosition in interface SequenceSite

setSequencePosition

public void setSequencePosition(int sequencePosition)

Specified by:

setSequencePosition in interface SequenceSite