org.biopax.paxtools.model.level2

Interface entity

All Superinterfaces:

BioPAXElement, Cloneable, InteractionParticipant, Level2Element, Serializable, XReferrable

All Known Subinterfaces:

biochemicalReaction, catalysis, complex, complexAssembly, control, conversion, dna, interaction, modulation, pathway, physicalEntity, physicalInteraction, process, protein, rna, sequenceEntity, smallMolecule, transport, transportWithBiochemicalReaction

public interface entity
extends Level2Element, XReferrable, InteractionParticipant

This class represents a discrete biological unit used when describing pathways. This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity.

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
void	addAVAILABILITY(String AVAILABILITY_TEXT) This method adds the given text to the avaialability set.
void	addDATA_SOURCE(dataSource DATA_SOURCE_INST) This method adds the given value to the DATA_SOURCE set.
void	addSYNONYMS(String SYNONYMS_TEXT) This method adds the given value to the SYNONYMS set.
Set<String>	getAVAILABILITY() The contents of this set can be modified but semantic consistency is not guaranteed.
Set<dataSource>	getDATA_SOURCE() This method returns a set of free text descriptions of the source of this data, e.g.
String	getNAME() This method returns the preferred full name for this entity.
String	getSHORT_NAME() This method sets an abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
Set<String>	getSYNONYMS() The contents of this set can be modified but semantic consistency is not guaranteed.
void	removeAVAILABILITY(String AVAILABILITY_TEXT) This method removes the given text from the avaialability set.
void	removeDATA_SOURCE(dataSource DATA_SOURCE_INST) This method removes the given value from the DATA_SOURCE set.
void	removeSYNONYMS(String SYNONYMS_TEXT) This method removes the given value from the SYNONYMS set.
void	setAVAILABILITY(Set<String> AVAILABILITY_TEXT) This method overrides existing set with the new set.
void	setDATA_SOURCE(Set<dataSource> DATA_SOURCE) This method overrides existing set with the new set.
void	setNAME(String NAME) This method sets the preferred full name for this entity to the given value.
void	setSHORT_NAME(String SHORT_NAME) An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
void	setSYNONYMS(Set<String> SYNONYMS) This method overrides existing set with the new set.

Methods inherited from interface org.biopax.paxtools.model.level2.XReferrable

addXREF, findCommonPublications, findCommonRelationships, findCommonUnifications, getXREF, removeXREF, setXREF

Methods inherited from interface org.biopax.paxtools.model.level2.InteractionParticipant

isPARTICIPANTSof

Methods inherited from interface org.biopax.paxtools.model.level2.Level2Element

addCOMMENT, getCOMMENT, removeCOMMENT, setCOMMENT

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

equivalenceCode, getAnnotations, getModelInterface, getUri, isEquivalent

Method Detail

addAVAILABILITY

void addAVAILABILITY(String AVAILABILITY_TEXT)

This method adds the given text to the avaialability set.

Parameters:

AVAILABILITY_TEXT - a string describing the availability of this data (e.g. a copyright statement).

addDATA_SOURCE

void addDATA_SOURCE(dataSource DATA_SOURCE_INST)

This method adds the given value to the DATA_SOURCE set.

Parameters:

DATA_SOURCE_INST - a free text description of the source of this data, e.g. a database or person name.

addSYNONYMS

void addSYNONYMS(String SYNONYMS_TEXT)

This method adds the given value to the SYNONYMS set.

Parameters:

SYNONYMS_TEXT - a new name to be added

getAVAILABILITY

Set<String> getAVAILABILITY()

The contents of this set can be modified but semantic consistency is not guaranteed. Using addAVAILABILITY(String) and removeAVAILABILITY(String) is recommended.

Returns:

a set of strings describing the availability of this data (e.g. a copyright statement).

getDATA_SOURCE

Set<dataSource> getDATA_SOURCE()

This method returns a set of free text descriptions of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation. The contents of this set can be modified but semantic consistency is not guaranteed. Using addDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) and removeDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) is recommended.

Returns:

a set of free text descriptions of the source of this data, e.g. a database or person name.

getNAME

String getNAME()

This method returns the preferred full name for this entity.

Returns:

preferred full name for this entity

getSHORT_NAME

String getSHORT_NAME()

This method sets an abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.

Returns:

an abbreviated name suitable for display.

getSYNONYMS

Set<String> getSYNONYMS()

The contents of this set can be modified but semantic consistency is not guaranteed. Using addSYNONYMS(java.lang.String) and removeSYNONYMS(java.lang.String) is recommended.

Returns:

a set of synonyms for the name of this entity. This should include the values of the NAME and SHORT-NAME property so that it is easy to find all known names in one place.

removeAVAILABILITY

void removeAVAILABILITY(String AVAILABILITY_TEXT)

This method removes the given text from the avaialability set.

Parameters:

AVAILABILITY_TEXT - a string describing the availability of this data (e.g. a copyright statement).

removeDATA_SOURCE

void removeDATA_SOURCE(dataSource DATA_SOURCE_INST)

This method removes the given value from the DATA_SOURCE set.

Parameters:

DATA_SOURCE_INST - a free text description of the source of this data, e.g. a database or person name.

removeSYNONYMS

void removeSYNONYMS(String SYNONYMS_TEXT)

This method removes the given value from the SYNONYMS set.

Parameters:

SYNONYMS_TEXT - a new name to be added

setAVAILABILITY

void setAVAILABILITY(Set<String> AVAILABILITY_TEXT)

This method overrides existing set with the new set. If you want to append to the existing set, use addAVAILABILITY(java.lang.String) instead.

Parameters:

AVAILABILITY_TEXT - a set of strings describing the availability of this data (e.g. a copyright statement).

setDATA_SOURCE

void setDATA_SOURCE(Set<dataSource> DATA_SOURCE)

This method overrides existing set with the new set. If you want to append to the existing set, use addDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) instead.

Parameters:

DATA_SOURCE - a set of free text descriptions of the source of this data, e.g. a database or person name.

setNAME

void setNAME(String NAME)

This method sets the preferred full name for this entity to the given value.

Parameters:

NAME - The preferred full name for this entity.

setSHORT_NAME

void setSHORT_NAME(String SHORT_NAME)

An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.

Parameters:

SHORT_NAME - new short name

setSYNONYMS

void setSYNONYMS(Set<String> SYNONYMS)

This method overrides existing set with the new set. If you want to append to the existing set, use addSYNONYMS(java.lang.String) instead.

Parameters:

SYNONYMS - a set of names for this entity.