Package org.biopax.paxtools.impl.level3

Class EntityImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.XReferrableImpl
org.biopax.paxtools.impl.level3.NamedImpl
org.biopax.paxtools.impl.level3.EntityImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, Entity, Level3Element, Named, Observable, XReferrable
Direct Known Subclasses:
GeneImpl, PhysicalEntityImpl, ProcessImpl
public abstract class EntityImpl extends NamedImpl implements Entity
See Also:

  • Constructor Details

    • EntityImpl

      public EntityImpl()
      Helper object for managing names

  • Method Details

    • getAvailability

      public Set<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).

    • addAvailability

      public void addAvailability(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(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).

    • getDataSource

      public Set<Provenance> getDataSource()
      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.addDataSource(Provenance) and Entity.removeDataSource(Provenance) is recommended.
      Specified by:
      getDataSource in interface Entity
      Returns:
      a set of free text descriptions of the source of this data, e.g. a database or person name.

    • setDataSource

      public void setDataSource(Set<Provenance> dataSource)

    • addDataSource

      public void addDataSource(Provenance dataSource)
      Description copied from interface: Entity
      This method adds the given value to the DATA_SOURCE set.
      Specified by:
      addDataSource in interface Entity
      Parameters:
      dataSource - a free text description of the source of this data, e.g. a database or person name.

    • removeDataSource

      public void removeDataSource(Provenance dataSource)
      Description copied from interface: Entity
      This method removes the given value from the DATA_SOURCE set.
      Specified by:
      removeDataSource in interface Entity
      Parameters:
      dataSource - a free text description of the source of this data, e.g. a database or person name.

    • getParticipantOf

      public Set<Interaction> getParticipantOf()
      Description copied from interface: Entity
      This method returns the interaction that this entity/pep takes part in. Contents of this set should not be modified. Reverse of Interaction.getParticipant()
      Specified by:
      getParticipantOf in interface Entity
      Returns:
      a set of interactions that

    • getEvidence

      public Set<Evidence> getEvidence()
      Specified by:
      getEvidence in interface Observable

    • addEvidence

      public void addEvidence(Evidence newEvidence)
      Specified by:
      addEvidence in interface Observable

    • removeEvidence

      public void removeEvidence(Evidence oldEvidence)
      Specified by:
      removeEvidence in interface Observable

    • semanticallyEquivalent

      protected boolean semanticallyEquivalent(BioPAXElement element)
      Overrides:
      semanticallyEquivalent in class BioPAXElementImpl