org.biopax.paxtools.model.level3
Interface FragmentFeature

All Superinterfaces:

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

All Known Implementing Classes:

FragmentFeatureImpl

public interface FragmentFeature
extends EntityFeature

Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.

Usage: Fragment Feature can be used to cover multiple types of modfications to the sequence of the physical entity:

• A protein with a single cleavage site that converts the protein into two fragments (e.g. pro-insulin converted to insulin and C-peptide). TODO: CV term for sequence fragment? PSI-MI CV term for cleavage site?
• A protein with two cleavage sites that removes an internal sequence e.g. an intein i.e. ABC -> A
• Cleavage of a circular sequence e.g. a plasmid.

In the case of removal ( e.g. intron) the fragment that is *removed* is specified in the feature location property. In the case of a "cut" (e.g. restriction enzyme cut site) the location of the cut is specified instead. Examples: Insulin Hormone

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

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