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:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, Level3Element, SequenceLocation, SequenceSite, UtilityClass

@Entity
@Indexed
public class SequenceSiteImpl
extends SequenceLocationImpl
implements SequenceSite

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

SequenceSiteImpl()

Method Summary

int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
java.lang.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)

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

addComment, getComment, removeComment, setComment

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

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, 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.Level3Element

addComment, getComment, removeComment

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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

SequenceSiteImpl

public SequenceSiteImpl()

Method Detail

getModelInterface

public java.lang.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.

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