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

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.alignment.template.Profile

Profile.StringFormat

Method Summary

Modifier and Type	Method	Description
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 java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface org.biojava.nbio.core.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

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