org.biopax.paxtools.impl.level2
Class entityImpl

java.lang.Object
  org.biopax.paxtools.impl.level2.bioPAXElementImpl
      org.biopax.paxtools.impl.level2.entityImpl

All Implemented Interfaces:

BioPAXElement, entity, InteractionParticipant, XReferrable

Direct Known Subclasses:

physicalEntityImpl, processImpl

public abstract class entityImpl
extends bioPAXElementImpl
implements entity

Field Summary

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

entityImpl()

Method Summary

void	addAVAILABILITY(java.lang.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(java.lang.String SYNONYMS_TEXT) This method adds the given value to the SYNONYMS set.
void	addXREF(xref XREF)
java.util.Set<java.lang.String>	getAVAILABILITY() The contents of this set can be modified but semantic consistency is not guaranteed.
java.util.Set<dataSource>	getDATA_SOURCE() This method returns a set of free text descriptions of the source of this data, e.g.
java.lang.String	getNAME() This method returns the preferred full name for this entity.
java.lang.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.
java.util.Set<java.lang.String>	getSYNONYMS() The contents of this set can be modified but semantic consistency is not guaranteed.
java.util.Set<xref>	getXREF()
java.util.Set<interaction>	isPARTICIPANTSof() This method returns the interaction that this entity/pep takes part in.
void	removeAVAILABILITY(java.lang.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(java.lang.String SYNONYMS_TEXT) This method removes the given value from the SYNONYMS set.
void	removeXREF(xref XREF)
void	setAVAILABILITY(java.util.Set<java.lang.String> AVAILABILITY) This method overrides existing set with the new set.
void	setDATA_SOURCE(java.util.Set<dataSource> DATA_SOURCE) This method overrides existing set with the new set.
void	setNAME(java.lang.String NAME) This method sets the preferred full name for this entity to the given value.
void	setSHORT_NAME(java.lang.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(java.util.Set<java.lang.String> SYNONYMS) This method overrides existing set with the new set.
void	setXREF(java.util.Set<xref> XREF)

Methods inherited from class org.biopax.paxtools.impl.level2.bioPAXElementImpl

addCOMMENT, equals, getCOMMENT, getRDFId, hashCode, removeCOMMENT, setCOMMENT, setRDFId

Methods inherited from class java.lang.Object

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

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

addCOMMENT, equivalenceCode, getCOMMENT, getModelInterface, getRDFId, isEquivalent, removeCOMMENT, setCOMMENT, setRDFId

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

addCOMMENT, equivalenceCode, getCOMMENT, getModelInterface, getRDFId, isEquivalent, removeCOMMENT, setCOMMENT, setRDFId

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

addCOMMENT, equivalenceCode, getCOMMENT, getModelInterface, getRDFId, isEquivalent, removeCOMMENT, setCOMMENT, setRDFId

Constructor Detail

entityImpl

public entityImpl()

Method Detail

getXREF

public java.util.Set<xref> getXREF()

Specified by:

getXREF in interface XReferrable

setXREF

public void setXREF(java.util.Set<xref> XREF)

Specified by:

setXREF in interface XReferrable

addXREF

public void addXREF(xref XREF)

Specified by:

addXREF in interface XReferrable

removeXREF

public void removeXREF(xref XREF)

Specified by:

removeXREF in interface XReferrable

getAVAILABILITY

public java.util.Set<java.lang.String> getAVAILABILITY()

Description copied from interface: entity

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

Specified by:

getAVAILABILITY in interface entity

Returns:

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

setAVAILABILITY

public void setAVAILABILITY(java.util.Set<java.lang.String> AVAILABILITY)

Description copied from interface: entity

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

Specified by:

setAVAILABILITY in interface entity

Parameters:

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

addAVAILABILITY

public void addAVAILABILITY(java.lang.String AVAILABILITY_TEXT)

Description copied from interface: entity

This method adds the given text to the avaialability set.

Specified by:

addAVAILABILITY in interface entity

Parameters:

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

removeAVAILABILITY

public void removeAVAILABILITY(java.lang.String AVAILABILITY_TEXT)

Description copied from interface: entity

This method removes the given text from the avaialability set.

Specified by:

removeAVAILABILITY in interface entity

Parameters:

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

getDATA_SOURCE

public java.util.Set<dataSource> getDATA_SOURCE()

Description copied from interface: entity

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 entity.addDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) and entity.removeDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) is recommended.

Specified by:

getDATA_SOURCE in interface entity

Returns:

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

setDATA_SOURCE

public void setDATA_SOURCE(java.util.Set<dataSource> DATA_SOURCE)

Description copied from interface: entity

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

Specified by:

setDATA_SOURCE in interface entity

Parameters:

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

addDATA_SOURCE

public void addDATA_SOURCE(dataSource DATA_SOURCE_INST)

Description copied from interface: entity

This method adds the given value to the DATA_SOURCE set.

Specified by:

addDATA_SOURCE in interface entity

Parameters:

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

removeDATA_SOURCE

public void removeDATA_SOURCE(dataSource DATA_SOURCE_INST)

Description copied from interface: entity

This method removes the given value from the DATA_SOURCE set.

Specified by:

removeDATA_SOURCE in interface entity

Parameters:

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

getNAME

public java.lang.String getNAME()

Description copied from interface: entity

This method returns the preferred full name for this entity.

Specified by:

getNAME in interface entity

Returns:

preferred full name for this entity

setNAME

public void setNAME(java.lang.String NAME)

Description copied from interface: entity

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

Specified by:

setNAME in interface entity

Parameters:

NAME - The preferred full name for this entity.

getSHORT_NAME

public java.lang.String getSHORT_NAME()

Description copied from interface: entity

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.

Specified by:

getSHORT_NAME in interface entity

Returns:

an abbreviated name suitable for display.

setSHORT_NAME

public void setSHORT_NAME(java.lang.String SHORT_NAME)

Description copied from interface: entity

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.

Specified by:

setSHORT_NAME in interface entity

getSYNONYMS

public java.util.Set<java.lang.String> getSYNONYMS()

Description copied from interface: entity

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

Specified by:

getSYNONYMS in interface entity

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.

setSYNONYMS

public void setSYNONYMS(java.util.Set<java.lang.String> SYNONYMS)

Description copied from interface: entity

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

Specified by:

setSYNONYMS in interface entity

Parameters:

SYNONYMS - a set of names for this entity.

addSYNONYMS

public void addSYNONYMS(java.lang.String SYNONYMS_TEXT)

Description copied from interface: entity

This method adds the given value to the SYNONYMS set.

Specified by:

addSYNONYMS in interface entity

Parameters:

SYNONYMS_TEXT - a new name to be added

removeSYNONYMS

public void removeSYNONYMS(java.lang.String SYNONYMS_TEXT)

Description copied from interface: entity

This method removes the given value from the SYNONYMS set.

Specified by:

removeSYNONYMS in interface entity

Parameters:

SYNONYMS_TEXT - a new name to be added

isPARTICIPANTSof

public java.util.Set<interaction> isPARTICIPANTSof()

Description copied from interface: InteractionParticipant

This method returns the interaction that this entity/pep takes part in. Contents of this set should not be modified.

Specified by:

isPARTICIPANTSof in interface InteractionParticipant

Returns:

a set of interactions that