org.biopax.paxtools.model.level3
Interface ExperimentalForm

All Superinterfaces:

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

All Known Implementing Classes:

ExperimentalFormImpl

public interface ExperimentalForm
extends UtilityClass

Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.

Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms

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

void	addExperimentalFeature(EntityFeature experimentalFeature) This method adds an experimental feature
void	addExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType) Adds an experimental form description.
java.util.Set<EntityFeature>	getExperimentalFeature() Contents of this set should not be modified.
java.util.Set<ExperimentalFormVocabulary>	getExperimentalFormDescription() Descriptor of this experimental form from a controlled vocabulary.
Entity	getExperimentalFormEntity()
void	removeExperimentalFeature(EntityFeature experimentalFeature) This method removes an experimental feature
void	removeExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType) Removes an experimental form description.
void	setExperimentalFormEntity(Entity newPARTICIPANT)

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

Method Detail

getExperimentalFormDescription

java.util.Set<ExperimentalFormVocabulary> getExperimentalFormDescription()

Descriptor of this experimental form from a controlled vocabulary. The contents of this set should not be modified. Use add/remove methods instead.

Returns:

a CV term from PSI-MI participant identification methdod, experimental role, experimental preparation.

addExperimentalFormDescription

void addExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)

Adds an experimental form description.

Parameters:

experimentalFormType - descriptor of this experimental form from a controlled vocabulary.

removeExperimentalFormDescription

void removeExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)

Removes an experimental form description.

Parameters:

experimentalFormType - descriptor of this experimental form from a controlled vocabulary.

getExperimentalFormEntity

Entity getExperimentalFormEntity()

Returns:

The gene or physical entity that this experimental form describes.

setExperimentalFormEntity

void setExperimentalFormEntity(Entity newPARTICIPANT)

getExperimentalFeature

java.util.Set<EntityFeature> getExperimentalFeature()

Contents of this set should not be modified. Please use add/remove methods instead.

Returns:

A feature of the experimental form of the participant of the interaction, such as a protein tag. It is not expected to occur in vivo or be necessary for the interaction.

addExperimentalFeature

void addExperimentalFeature(EntityFeature experimentalFeature)

This method adds an experimental feature

Parameters:

experimentalFeature - of the experimental form of the participant of the interaction, such as a protein tag. It is not expected to occur in vivo or be necessary for the interaction.

removeExperimentalFeature

void removeExperimentalFeature(EntityFeature experimentalFeature)

This method removes an experimental feature

Parameters:

experimentalFeature - of the experimental form of the participant of the interaction, such as a protein tag. It is not expected to occur in vivo or be necessary for the interaction.