Interface BioEntry

    • Method Detail

      • getNamespace

        Namespace getNamespace()
        Returns the namespace of this bioentry. The namespace is supposed to be an immutable property set by the constructor.
        Returns:
        the namespace of this bioentry.
      • getName

        java.lang.String getName()
        Returns the name of this bioentry. The name is supposed to be an immutable property set by the constructor.
        Returns:
        Value of property name.
      • getAccession

        java.lang.String getAccession()
        Returns the accession of this bioentry. The accession is supposed to be an immutable property set by the constructor.
        Returns:
        Value of property accession.
      • getIdentifier

        java.lang.String getIdentifier()
        Returns the identifier of this bioentry.
        Returns:
        Value of property identifier.
      • setIdentifier

        void setIdentifier​(java.lang.String identifier)
                    throws ChangeVetoException
        Sets the identifier of this bioentry. Null is allowable.
        Parameters:
        identifier - New value of property identifier.
        Throws:
        ChangeVetoException - in case of objections.
      • getDivision

        java.lang.String getDivision()
        Returns the division of this bioentry. Division relates to a division of the parent namespace.
        Returns:
        Value of property division.
      • setDivision

        void setDivision​(java.lang.String division)
                  throws ChangeVetoException
        Sets the division of this bioentry. Null is allowable.
        Parameters:
        division - New value of property division.
        Throws:
        ChangeVetoException - in case of objections.
      • getDescription

        java.lang.String getDescription()
        Returns a description of this sequence.
        Returns:
        Value of property description.
      • setDescription

        void setDescription​(java.lang.String description)
                     throws ChangeVetoException
        Sets the description for this bioentry.
        Parameters:
        description - New value of property description.
        Throws:
        ChangeVetoException - in case of objections.
      • getVersion

        int getVersion()
        Gets the version of this bioentry. Bioentries with no versions return 0. The version is supposed to be immutable and set only by the constructor.
        Returns:
        Value of property version.
      • getTaxon

        NCBITaxon getTaxon()
        Gets the taxon associated with this bioentry. It may be null.
        Returns:
        Value of property taxon.
      • setTaxon

        void setTaxon​(NCBITaxon taxon)
               throws ChangeVetoException
        Sets the taxon for this bioentry. It may be null, in which case the taxon is unset.
        Parameters:
        taxon - New value of property taxon.
        Throws:
        ChangeVetoException - in case of objections.
      • getRankedDocRefs

        java.util.Set getRankedDocRefs()
        Returns a set of all bioentrydocrefs associated with this bioentry. This set is not mutable. If no docrefs are associated, you will get back an empty set.
        Returns:
        a set of RankedDocRef objects.
        See Also:
        RankedDocRef
      • getComments

        java.util.Set getComments()
        Returns a set of all comments associated with this bioentry. This set is not mutable. If no comments are associated, you will get back an empty set.
        Returns:
        a set of Comment objects.
        See Also:
        Comment
      • getRelationships

        java.util.Set getRelationships()
        Returns a set of all relationships associated with this bioentry. This set is not mutable. If no relationships are associated, you will get back an empty set.
        Returns:
        a set of BioEntryRelationship objects.
        See Also:
        BioEntryRelationship
      • addRankedDocRef

        void addRankedDocRef​(RankedDocRef docref)
                      throws ChangeVetoException
        Adds a ranked docref instance to this bioentry. Must not be null.
        Parameters:
        docref - the item to add.
        Throws:
        ChangeVetoException - if it doesn't want to add it.
      • removeRankedDocRef

        void removeRankedDocRef​(RankedDocRef docref)
                         throws ChangeVetoException
        Removes a ranked docref instance from this bioentry. If it was not found, nothing happens.
        Parameters:
        docref - the item to remove.
        Throws:
        ChangeVetoException - if it doesn't want to remove it.
      • addComment

        void addComment​(Comment comment)
                 throws ChangeVetoException
        Adds a comment instance to this bioentry. Must not be null.
        Parameters:
        comment - the item to add.
        Throws:
        ChangeVetoException - if it doesn't want to add it.
      • removeComment

        void removeComment​(Comment comment)
                    throws ChangeVetoException
        Removes a comment instance from this bioentry. If it wasn't present, it nothing will happen.
        Parameters:
        comment - the item to remove.
        Throws:
        ChangeVetoException - if it doesn't want to remove it.
      • removeRelationship

        void removeRelationship​(BioEntryRelationship relation)
                         throws ChangeVetoException
        Removes a relation instance from this bioentry. If it wasn't present, nothing will happen.
        Parameters:
        relation - the item to remove.
        Throws:
        ChangeVetoException - if it doesn't want to remove it.