Package org.biojava.nbio.core.alignment.template

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:
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 Details

    • 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