Package org.biojavax

Interface RankedDocRef

All Superinterfaces:
Changeable, Comparable
All Known Implementing Classes:
SimpleRankedDocRef
public interface RankedDocRef extends Comparable, Changeable
Represents a documentary reference. Relates to the bioentryreference table in BioSQL.
Since:
1.5
Author:
Richard Holland, gwaldon
See Also:

  • Field Details

  • Method Details

    • 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

      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

      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.

    • setLocation

      void setLocation(RichLocation location) throws ChangeVetoException
      Set the location of this reference.
      Parameters:
      location - the location to use.
      Throws:
      ChangeVetoException - if the new location is unacceptable.

    • 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.