org.biopax.paxtools.model.level3
Interface ModificationFeature

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, EntityFeature, Level3Element, Observable, java.io.Serializable, UtilityClass

All Known Subinterfaces:

CovalentBindingFeature

All Known Implementing Classes:

CovalentBindingFeatureImpl, ModificationFeatureImpl

public interface ModificationFeature
extends EntityFeature

Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification. The difference between this class and BindingFeature is that this is covalent and BindingFeature is non-covalent.

Rationale: In Biology, identity of DNA, RNA and Protein entities are defined around a wildtype sequence. Covalent modifications to this basal sequence are represented using modificaton features. Since small molecules are identified based on their chemical structure, not sequence, a covalent modification to a small molecule would result in a different molecule.

Examples: A phosphorylation feature on a protein that enables the binding of an SH2 domain.

Usagee: The added groups should be simple and stateless, such as phosphate or methyl groups and are captured by the modificationType controlled vocabulary. In other cases, such as covalently linked proteins, use CovalentBindingFeature instead. SmallMolecules can only have covalentBindingFeatures.

Nested Class Summary

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

BioPAXElement.Key

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

SequenceModificationVocabulary	getModificationType()
void	setModificationType(SequenceModificationVocabulary featureType)

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.Level3Element

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

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

addEvidence, getEvidence, removeEvidence

Method Detail

getModificationType

SequenceModificationVocabulary getModificationType()

Returns:

Description and classification of the feature.

setModificationType

void setModificationType(SequenceModificationVocabulary featureType)

Parameters:

featureType - Description and classification of the feature.