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:

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

@Entity
@Indexed
public class ExperimentalFormImpl
extends L3ElementImpl
implements ExperimentalForm

See Also:

Serialized Form

Nested Class Summary

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

BioPAXElement.Key

Field Summary

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

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

ExperimentalFormImpl()
Constructor.

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()
java.lang.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	setExperimentalFeature(java.util.Set<EntityFeature> experimentalFeature)
void	setExperimentalFormDescription(java.util.Set<ExperimentalFormVocabulary> experimentalFormDescription)
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

equivalenceCode, getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, semanticallyEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

addComment, getComment, removeComment

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

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

ExperimentalFormImpl

public ExperimentalFormImpl()

Constructor.

Method Detail

getModelInterface

public java.lang.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 java.util.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.

setExperimentalFormDescription

public void setExperimentalFormDescription(java.util.Set<ExperimentalFormVocabulary> experimentalFormDescription)

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 java.util.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.

setExperimentalFeature

public void setExperimentalFeature(java.util.Set<EntityFeature> experimentalFeature)

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.