Package org.biojava.nbio.core.sequence.location

Class SequenceLocation<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.location.template.AbstractLocation

org.biojava.nbio.core.sequence.location.SimpleLocation

org.biojava.nbio.core.sequence.location.SequenceLocation<S,C>

All Implemented Interfaces:

Serializable, Iterable<Location>, Location, Accessioned

public class SequenceLocation<S extends AbstractSequence<C>,C extends Compound>
extends SimpleLocation

A location in a sequence that keeps a reference to its parent sequence

Author:

Scooter Willis , Paolo Pavan

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.Location

Location.Tools

Field Summary

Fields inherited from interface org.biojava.nbio.core.sequence.location.template.Location

EMPTY

Constructor Summary

Constructors

Constructor	Description
SequenceLocation(int start, int end, S sequence)
SequenceLocation(int start, int end, S sequence, Strand strand)
SequenceLocation(int start, int end, S sequence, Strand strand, boolean circular, List<Location> subLocations)
SequenceLocation(Point start, Point end, S sequence, Strand strand)

Method Summary

Modifier and Type	Method	Description
S	getSequence()
void	setSequence(S sequence)

Methods inherited from class org.biojava.nbio.core.sequence.location.template.AbstractLocation

assertLocation, canComplement, equals, getAccession, getEnd, getLength, getRelevantSubLocations, getRelevantSubSequence, getStart, getStrand, getSubLocations, getSubSequence, hashCode, isBetweenCompounds, isCircular, isComplex, isPartial, isPartialOn3prime, isPartialOn5prime, iterator, reverseSequence, setAccession, setBetweenCompounds, setCircular, setEnd, setPartialOn3prime, setPartialOn5prime, setStart, setStrand, setSubLocations, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

SequenceLocation

public SequenceLocation(int start,
                        int end,
                        S sequence)

SequenceLocation

public SequenceLocation(int start,
                        int end,
                        S sequence,
                        Strand strand,
                        boolean circular,
                        List<Location> subLocations)

SequenceLocation

public SequenceLocation(int start,
                        int end,
                        S sequence,
                        Strand strand)

SequenceLocation

public SequenceLocation(Point start,
                        Point end,
                        S sequence,
                        Strand strand)

Method Detail

getSequence

public S getSequence()

Returns:

the sequence

setSequence

public void setSequence(S sequence)