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

Class AbstractLocation

java.lang.Object

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

All Implemented Interfaces:

Serializable, Iterable<Location>, Location, Accessioned

Direct Known Subclasses:

InsdcLocations.BondLocation, InsdcLocations.OneOfLocation, SimpleLocation

public abstract class AbstractLocation
extends Object
implements Serializable, Location

Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand

Author:

ayates, 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

Modifier	Constructor and Description
protected	AbstractLocation()
	AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, List<Location> subLocations) Default constructor
	AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations) Default constructor

Method Summary

Modifier and Type	Method and Description
protected void	assertLocation()
protected <C extends Compound> boolean	canComplement(Sequence<C> sequence) Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
boolean	equals(Object obj)
AccessionID	getAccession() Returns the AccessionID this location is currently bound with
Point	getEnd() End of the location
int	getLength() Returns the length of the outer bounds of this location
List<Location>	getRelevantSubLocations() Returns the normalised list of sub locations i.e.
<C extends Compound> Sequence<C>	getRelevantSubSequence(Sequence<C> sequence) Will return a SequenceReader object which offers a view of all resolved locations i.e.
Point	getStart() Start of the location
Strand	getStrand() Strand which the location is located on
List<Location>	getSubLocations() Gives access to the sub locations for this location.
<C extends Compound> Sequence<C>	getSubSequence(Sequence<C> sequence) If circular this will return the sequence represented by the sub locations joined.
int	hashCode()
boolean	isBetweenCompounds() Returns true if the position is meant to represent a point between two points such as 78^79.
boolean	isCircular() Indicates if this location is circular.
boolean	isComplex() Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
boolean	isPartial()
boolean	isPartialOn3prime()
boolean	isPartialOn5prime()
Iterator<Location>	iterator() Iterates through all known sub-locations for this location but does not descend
protected <C extends Compound> Sequence<C>	reverseSequence(Sequence<C> sequence) Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).
void	setAccession(AccessionID accession)
void	setBetweenCompounds(boolean betweenCompounds)
protected void	setCircular(boolean circular)
protected void	setEnd(Point end)
void	setPartialOn3prime(boolean partialOn3prime)
void	setPartialOn5prime(boolean partialOn5prime)
protected void	setStart(Point start)
void	setStrand(Strand strand)
void	setSubLocations(List<Location> subLocations)
String	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

AbstractLocation

protected AbstractLocation()

AbstractLocation

public AbstractLocation(Point start,
                        Point end,
                        Strand strand,
                        boolean circular,
                        boolean betweenCompounds,
                        List<Location> subLocations)

Default constructor

Parameters:

start - start of the location

end - end of the location

strand - strand it is located on

circular - Boolean which says if the current location was circular or not

betweenCompounds - Indicates the location lies at the position between a pair of bases; means the bases must be next to each other (and therefore cannot be complex)

subLocations - Sub locations which composes this location

AbstractLocation

public AbstractLocation(Point start,
                        Point end,
                        Strand strand,
                        boolean circular,
                        boolean betweenCompounds,
                        AccessionID accession,
                        List<Location> subLocations)

Default constructor

Parameters:

start - start of the location

end - end of the location

strand - strand it is located on

circular - Boolean which says if the current location was circular or not

betweenCompounds - Indicates the location lies at the position between a pair of bases; means the bases must be next to each other (and therefore cannot be complex)

accession - The accession ID to link this location to

subLocations - Sub locations which composes this location

Method Detail

assertLocation

protected void assertLocation()

getEnd

public Point getEnd()

Description copied from interface: Location

End of the location

Specified by:

getEnd in interface Location

getStart

public Point getStart()

Description copied from interface: Location

Start of the location

Specified by:

getStart in interface Location

getLength

public int getLength()

Description copied from interface: Location

Returns the length of the outer bounds of this location

Specified by:

getLength in interface Location

getStrand

public Strand getStrand()

Description copied from interface: Location

Strand which the location is located on

Specified by:

getStrand in interface Location

getSubLocations

public List<Location> getSubLocations()

Description copied from interface: Location

Gives access to the sub locations for this location. However this does not return sub-locations of sub-locations. For that functionality use #getAllSubLocations().

Specified by:

getSubLocations in interface Location

Returns:

A list of a single level of sub-locations

isComplex

public boolean isComplex()

Description copied from interface: Location

Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.

Specified by:

isComplex in interface Location

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

isPartialOn5prime

public boolean isPartialOn5prime()

setPartialOn5prime

public void setPartialOn5prime(boolean partialOn5prime)

isPartialOn3prime

public boolean isPartialOn3prime()

setPartialOn3prime

public void setPartialOn3prime(boolean partialOn3prime)

isPartial

public boolean isPartial()

iterator

public Iterator<Location> iterator()

Iterates through all known sub-locations for this location but does not descend

Specified by:

iterator in interface Iterable<Location>

getRelevantSubLocations

public List<Location> getRelevantSubLocations()

Returns the normalised list of sub locations i.e. only those locations which do not have a sub location. Useful for when you need to get the exact elements of a location back for sub sequences.

Specified by:

getRelevantSubLocations in interface Location

Returns:

List of all sub locations including sub-locations of sub locations

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

isCircular

public boolean isCircular()

Description copied from interface: Location

Indicates if this location is circular.

Specified by:

isCircular in interface Location

isBetweenCompounds

public boolean isBetweenCompounds()

Description copied from interface: Location

Returns true if the position is meant to represent a point between two points such as 78^79. Only valid if start and stop are next to each other.

Specified by:

isBetweenCompounds in interface Location

getSubSequence

public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)

If circular this will return the sequence represented by the sub locations joined. If not circular then we get the Sequence for the outer-bounds defined by this location.

Specified by:

getSubSequence in interface Location

Parameters:

sequence - The sequence object to work with

Returns:

The sequence

getRelevantSubSequence

public <C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)

Description copied from interface: Location

Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented

Specified by:

getRelevantSubSequence in interface Location

Parameters:

sequence - The sequence object to work with

Returns:

The full assembled sequence

reverseSequence

protected <C extends Compound> Sequence<C> reverseSequence(Sequence<C> sequence)

Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists). Also does checking to see if the location we are on is on the reverse strand or not.

canComplement

protected <C extends Compound> boolean canComplement(Sequence<C> sequence)

Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement

toString

public String toString()

Overrides:

toString in class Object

setCircular

protected void setCircular(boolean circular)

setEnd

protected void setEnd(Point end)

setStart

protected void setStart(Point start)

setStrand

public void setStrand(Strand strand)

setBetweenCompounds

public void setBetweenCompounds(boolean betweenCompounds)

setSubLocations

public void setSubLocations(List<Location> subLocations)

setAccession

public void setAccession(AccessionID accession)