Package org.biopax.paxtools.impl.level3

Class ExperimentalFormImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.ExperimentalFormImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ExperimentalForm, Level3Element, UtilityClass

public class ExperimentalFormImpl
extends L3ElementImpl
implements ExperimentalForm

See Also:

• Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor	Description
ExperimentalFormImpl()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addExperimentalFeature(EntityFeature experimentalFeature)	This method adds an experimental feature
void	addExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)	Adds an experimental form description.
Set<EntityFeature>	getExperimentalFeature()	Contents of this set should not be modified.
Set<ExperimentalFormVocabulary>	getExperimentalFormDescription()	Descriptor of this experimental form from a controlled vocabulary.
Entity	getExperimentalFormEntity()
Class<? extends ExperimentalForm>	getModelInterface()	This method returns the actual model interface that a class implements.
void	removeExperimentalFeature(EntityFeature experimentalFeature)	This method removes an experimental feature
void	removeExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)	Removes an experimental form description.
void	setExperimentalFormEntity(Entity experimentalFormEntity)

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

addComment, getComment, removeComment, setComment

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

equals, equivalenceCode, getAnnotations, getUri, hashCode, isEquivalent, semanticallyEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

equivalenceCode, getAnnotations, getUri, isEquivalent

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Constructor Details

ExperimentalFormImpl

public ExperimentalFormImpl()

Constructor.

Method Details

getModelInterface

public Class<? extends ExperimentalForm> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

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

getExperimentalFormDescription

public Set<ExperimentalFormVocabulary> getExperimentalFormDescription()

Description copied from interface: ExperimentalForm

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

Specified by:

getExperimentalFormDescription in interface ExperimentalForm

Returns:

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

addExperimentalFormDescription

public void addExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)

Description copied from interface: ExperimentalForm

Adds an experimental form description.

Specified by:

addExperimentalFormDescription in interface ExperimentalForm

Parameters:

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

removeExperimentalFormDescription

public void removeExperimentalFormDescription(ExperimentalFormVocabulary experimentalFormType)

Description copied from interface: ExperimentalForm

Removes an experimental form description.

Specified by:

removeExperimentalFormDescription in interface ExperimentalForm

Parameters:

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

getExperimentalFormEntity

public Entity getExperimentalFormEntity()

Specified by:

getExperimentalFormEntity in interface ExperimentalForm

Returns:

The gene or physical entity that this experimental form describes.

setExperimentalFormEntity

public void setExperimentalFormEntity(Entity experimentalFormEntity)

Specified by:

setExperimentalFormEntity in interface ExperimentalForm

getExperimentalFeature

public Set<EntityFeature> getExperimentalFeature()

Description copied from interface: ExperimentalForm

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

Specified by:

getExperimentalFeature in interface ExperimentalForm

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

public void addExperimentalFeature(EntityFeature experimentalFeature)

Description copied from interface: ExperimentalForm

This method adds an experimental feature

Specified by:

addExperimentalFeature in interface ExperimentalForm

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

public void removeExperimentalFeature(EntityFeature experimentalFeature)

Description copied from interface: ExperimentalForm

This method removes an experimental feature

Specified by:

removeExperimentalFeature in interface ExperimentalForm

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.