org.biopax.paxtools.impl.level3

Class ModificationFeatureImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.EntityFeatureImpl

org.biopax.paxtools.impl.level3.ModificationFeatureImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, EntityFeature, Level3Element, ModificationFeature, Observable, UtilityClass

@Entity
 @Indexed
public class ModificationFeatureImpl
extends EntityFeatureImpl
implements ModificationFeature

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
ModificationFeatureImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Class<? extends ModificationFeature>	getModelInterface() This method returns the actual model interface that a class implements.
SequenceModificationVocabulary	getModificationType()
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setModificationType(SequenceModificationVocabulary featureType)
String	toString()

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

addEvidence, addMemberFeature, atEquivalentLocation, getEntityFeatureOf, getEvidence, getFeatureLocation, getFeatureLocationType, getFeatureOf, getMemberFeature, getMemberFeatureOf, getNotFeatureOf, locationCode, removeEvidence, removeMemberFeature, setEntityFeatureOf, setEvidence, setFeatureLocation, setFeatureLocationType, setFeatureOf, setMemberFeature, setMemberFeatureOf, setNotFeatureOf

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, getAnnotations, getPk, getRDFId, 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.level3.EntityFeature

addMemberFeature, atEquivalentLocation, getEntityFeatureOf, getFeatureLocation, getFeatureLocationType, getFeatureOf, getMemberFeature, getMemberFeatureOf, getNotFeatureOf, removeMemberFeature, setFeatureLocation, setFeatureLocationType

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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

ModificationFeatureImpl

public ModificationFeatureImpl()

Method Detail

toString

public String toString()

Overrides:

toString in class BioPAXElementImpl

getModelInterface

public Class<? extends ModificationFeature> 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 EntityFeatureImpl

Returns:

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

getModificationType

public SequenceModificationVocabulary getModificationType()

Specified by:

getModificationType in interface ModificationFeature

Returns:

Description and classification of the feature.

setModificationType

public void setModificationType(SequenceModificationVocabulary featureType)

Specified by:

setModificationType in interface ModificationFeature

Parameters:

featureType - Description and classification of the feature.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class EntityFeatureImpl

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 EntityFeatureImpl

Returns:

an integer that is same across all equivalent entities.