Package org.biojavax

Interface RankedDocRef

  • All Superinterfaces:
    Changeable, java.lang.Comparable
    All Known Implementing Classes:
    SimpleRankedDocRef

    public interface RankedDocRef
    extends java.lang.Comparable, Changeable
    Represents a documentary reference. Relates to the bioentryreference table in BioSQL.
    Since:
    1.5
    Author:
    Richard Holland, gwaldon
    See Also:
    DocRef
    • Method Detail

      • getDocumentReference

        DocRef getDocumentReference()
        Represents a reference to a document. This value is intended to be set by the constructor of the implementing class.
        Returns:
        the document reference.
      • getStart

        java.lang.Integer getStart()
        The start position in the sequence that this reference is referred to from. This value is intended to be set by the constructor of the implementing class. The position returned is from 1 to the length of the sequence.
        Returns:
        the start position.
      • getEnd

        java.lang.Integer getEnd()
        The end position in the sequence that this reference is referred to from. This value is intended to be set by the constructor of the implementing class. The position returned is from 1 to the length of the sequence.
        Returns:
        the end position.
      • getLocation

        RichLocation getLocation()
        If this object was constructed using a location instead of two integers, then this method will return that location. The getStart() and getEnd() methods will then return the min and max of that location, using the default location position resolver to resolve them to exact positions. If this object was constructed using two integers, then this method will return a simple location whose min and max correspond to those integers.
        Returns:
        the location of this reference on the sequence.
      • getRank

        int getRank()
        The rank of this reference. This value is intended to be set by the constructor of the implementing class.
        Returns:
        the rank.
      • setRank

        void setRank​(int rank)
              throws ChangeVetoException
        Set the rank of this reference.
        Parameters:
        rank - the rank to use.
        Throws:
        ChangeVetoException - if the new rank is unacceptable.