org.biojava.nbio.core.sequence.views

Class ReversedSequenceView<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.template.SequenceProxyView<C>

org.biojava.nbio.core.sequence.views.ReversedSequenceView<C>

Type Parameters:

C - Must be a subtype of @{link Compound}

All Implemented Interfaces:

Iterable<C>, Accessioned, Sequence<C>, SequenceView<C>

public class ReversedSequenceView<C extends Compound>
extends SequenceProxyView<C>

For a given sequence this class will return the base at the reversed position i.e. in a sequence of size 10, if you request base 2 you will get back the base at position 9. Sub-views can be made of this class which also respect the reversed calls.

Author:

Andy Yates

Constructor Summary

Constructors

Constructor and Description
ReversedSequenceView(Sequence<C> sequence)

Method Summary

Modifier and Type	Method and Description
C	getCompoundAt(int position) Returns the Compound at the given biological index
String	getSequenceAsString() Returns the String representation of the Sequence
protected int	toIndex(int index)

Methods inherited from class org.biojava.nbio.core.sequence.template.SequenceProxyView

countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

ReversedSequenceView

public ReversedSequenceView(Sequence<C> sequence)

Method Detail

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

Overrides:

getSequenceAsString in class SequenceProxyView<C extends Compound>

toIndex

protected int toIndex(int index)

getCompoundAt

public C getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

Overrides:

getCompoundAt in class SequenceProxyView<C extends Compound>

Parameters:

position - Biological index (1 to n)

Returns:

Compound at the specified position