Interface ProfileView<S extends Sequence<C>,​C extends Compound>

  • Type Parameters:
    S - each element of the alignment Profile is of type S
    C - each element of an AlignedSequence is a Compound of type C
    All Superinterfaces:
    java.lang.Iterable<AlignedSequence<S,​C>>, Profile<S,​C>

    public interface ProfileView<S extends Sequence<C>,​C extends Compound>
    extends Profile<S,​C>
    Defines a data structure for a view of sequence alignment.
    Author:
    Mark Chapman, Paolo Pavan
    • Method Detail

      • getEnd

        int getEnd()
        Returns the column index of the viewed Profile corresponding to the final element in this view
        Returns:
        column index of this view's final element
      • getStart

        int getStart()
        Returns the column index of the viewed Profile corresponding to the first element in this view
        Returns:
        column index of this view's first element
      • getViewedProfile

        Profile<S,​C> getViewedProfile()
        Returns the entire Profile being viewed
        Returns:
        the entire alignment profile