org.biojava3.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

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile
Profile.StringFormat
 
Method Summary
 int getEnd()
          Returns the column index of the viewed Profile corresponding to the final element in this view
 int getStart()
          Returns the column index of the viewed Profile corresponding to the first element in this view
 Profile<S,C> getViewedProfile()
          Returns the entire Profile being viewed
 
Methods inherited from interface org.biojava3.alignment.template.Profile
getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, toString, toString, toString
 
Methods inherited from interface java.lang.Iterable
iterator
 

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