Package org.biopax.paxtools.impl.level3

Class EntityFeatureImpl

java.lang.Object
org.biopax.paxtools.impl.BioPAXElementImpl
org.biopax.paxtools.impl.level3.L3ElementImpl
org.biopax.paxtools.impl.level3.EntityFeatureImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, EntityFeature, Level3Element, Observable, UtilityClass
Direct Known Subclasses:
BindingFeatureImpl, FragmentFeatureImpl, ModificationFeatureImpl
public class EntityFeatureImpl extends L3ElementImpl implements EntityFeature
See Also:

  • Constructor Details

    • EntityFeatureImpl

      public EntityFeatureImpl()

  • Method Details

    • getModelInterface

      public Class<? extends EntityFeature> 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.

    • getEntityFeatureOf

      public EntityReference getEntityFeatureOf()
      Description copied from interface: EntityFeature
      Inverse of EntityReference.getEntityFeature()
      Specified by:
      getEntityFeatureOf in interface EntityFeature
      Returns:
      the EntityReference that this EntityFeature belongs to.

    • setEntityFeatureOf

      public void setEntityFeatureOf(EntityReference entityReference)

    • getFeatureOf

      public Set<PhysicalEntity> getFeatureOf()
      Description copied from interface: EntityFeature
      Inverse of PhysicalEntity.getFeature() Contents of this set is generated automatically and should not be modified.
      Specified by:
      getFeatureOf in interface EntityFeature
      Returns:
      The list of PhysicalEntities that were observed to have this feature.

    • getNotFeatureOf

      public Set<PhysicalEntity> getNotFeatureOf()
      Description copied from interface: EntityFeature
      Inverse of PhysicalEntity.getNotFeature() Contents of this set is generated automatically and should not be modified.
      Specified by:
      getNotFeatureOf in interface EntityFeature
      Returns:
      The list of PhysicalEntities that were observed to NOT have this feature.

    • getEvidence

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

    • addEvidence

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

    • removeEvidence

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

    • getFeatureLocation

      public SequenceLocation getFeatureLocation()
      Description copied from interface: EntityFeature
      Location of the feature on the sequence of the interactor. For modification features this is the modified base or residue. For binding features this is the binding site and for fragment features this is the location of the fragment on the "base" sequence. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence. Small Molecules can have binding features but currently it is not possible to define the binding site on the small molecules. In those cases this property should not be specified.
      Specified by:
      getFeatureLocation in interface EntityFeature
      Returns:
      Location of the feature on the sequence of the interactor.

    • setFeatureLocation

      public void setFeatureLocation(SequenceLocation featureLocation)
      Description copied from interface: EntityFeature
      Location of the feature on the sequence of the interactor. For modification features this is the modified base or residue. For binding features this is the binding site and for fragment features this is the location of the fragment on the "base" sequence. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence. Small Molecules can have binding features but currently it is not possible to define the binding site on the small molecules. In those cases this property should not be specified.
      Specified by:
      setFeatureLocation in interface EntityFeature
      Parameters:
      featureLocation - of the feature

    • getFeatureLocationType

      public SequenceRegionVocabulary getFeatureLocationType()
      Description copied from interface: EntityFeature
      A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain. Using Sequence Ontology (http://www.sequenceontology.org) is recommended.
      Specified by:
      getFeatureLocationType in interface EntityFeature
      Returns:
      A CV term describing the location of the feature

    • setFeatureLocationType

      public void setFeatureLocationType(SequenceRegionVocabulary regionVocabulary)
      Description copied from interface: EntityFeature
      A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain. Using Sequence Ontology (http://www.sequenceontology.org) is recommended.
      Specified by:
      setFeatureLocationType in interface EntityFeature
      Parameters:
      regionVocabulary - A CV term describing the location of the feature

    • getMemberFeature

      public Set<EntityFeature> getMemberFeature()
      Description copied from interface: EntityFeature
      An entity feature that belongs to this homology grouping. Members of this set should be of the same class of this EntityFeature. Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature. If this set is not empty than the sequenceLocation of this feature should be null. Example: a homologous phosphorylation site across a protein family.
      Specified by:
      getMemberFeature in interface EntityFeature
      Returns:
      An entity feature that belongs to this homology grouping.

    • addMemberFeature

      public void addMemberFeature(EntityFeature feature)
      Description copied from interface: EntityFeature
      An entity feature that belongs to this homology grouping. Members of this set should be of the same class of this EntityFeature. Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature. If this set is not empty than the sequenceLocation of this feature should be null. Example: a homologous phosphorylation site across a protein family.
      Specified by:
      addMemberFeature in interface EntityFeature
      Parameters:
      feature - An entity feature that belongs to this homology grouping.

    • removeMemberFeature

      public void removeMemberFeature(EntityFeature feature)
      Description copied from interface: EntityFeature
      An entity feature that belongs to this homology grouping. Members of this set should be of the same class of this EntityFeature. Members of this set should be an EntityFeature of an EntityReference which is a memberEntityReference of the EntityReference of this feature. If this set is not empty than the sequenceLocation of this feature should be null. Example: a homologous phosphorylation site across a protein family.
      Specified by:
      removeMemberFeature in interface EntityFeature
      Parameters:
      feature - An entity feature that belongs to this homology grouping.

    • getMemberFeatureOf

      public Set<EntityFeature> getMemberFeatureOf()
      Description copied from interface: EntityFeature
      Reverse of EntityFeature.getMemberFeature()
      Specified by:
      getMemberFeatureOf in interface EntityFeature
      Returns:
      the generic feature(s) that this feature belong to

    • atEquivalentLocation

      public boolean atEquivalentLocation(EntityFeature that)
      This method returns true if and only if two entity features are on the same known location on a known ER. Unknown location or ER on any one of the features results in a false.
      Specified by:
      atEquivalentLocation in interface EntityFeature
      Parameters:
      that - EntityFeature to be compared
      Returns:
      returns true iff the given feature is at the equivalent sequence location with this feature

    • locationCode

      protected int locationCode()

    • semanticallyEquivalent

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

    • equivalenceCode

      public int equivalenceCode()
      Description copied from interface: BioPAXElement
      If two elements are equivalent, then their equivalence code should be the same.
      Specified by:
      equivalenceCode in interface BioPAXElement
      Overrides:
      equivalenceCode in class BioPAXElementImpl
      Returns:
      an integer that is same across all equivalent entities.