org.biojava.bio.symbol

Class CircularLocation

java.lang.Object

org.biojava.bio.symbol.AbstractLocationDecorator

org.biojava.bio.symbol.CircularLocation

All Implemented Interfaces:

Location

public class CircularLocation
extends AbstractLocationDecorator

Circular view onto an underlying Location instance. If the location overlaps the origin of the sequence the underlying location will be a CompoundLocation Note that in this case isContiguous() will return false. This behaviour is desirable for proper treatment of the location with LocationTools. To find if a location overlaps the origin use the overlapsOrigin() method

Note also that as a location that overlaps the origin is a compound location it's min will be 1 and its max will be length (by default). In these cases it is imperative to use the block iterator if you wish to know the 'true' min and max (bearing in mind that there is no logical value for a min or max on a circular sequence).

The symbols() method has been overridden to handle the weirdness of a location crossing the origin.

Since:

1.2

Author:

Matthew Pocock, Mark Schreiber

Field Summary

Fields inherited from interface org.biojava.bio.symbol.Location

empty, full, naturalOrder

Constructor Summary

Constructors

Constructor and Description
CircularLocation(Location wrapped, int length) Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations
CircularLocation(Location wrapped, int length, int fivePrimeEnd) Makes a CircularLocation where the 5' end of the Location is specified.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	contains(int p) Checks if this location contains a point.
boolean	contains(Location l) Checks if this location contains the other.
protected Location	decorate(Location loc)
boolean	equals(Object o) Checks if this location is equivalent to the other.
ListIterator	fivePrimeBlockIterator() Iterates over the location blocks in order starting with the most 5'
int	get3PrimeEnd()
int	get5PrimeEnd() The point at which indicates the 5' end of the Location.
int	getLength()
int	getMax() This will give you the coordinate of the maximum point contained by this Location.
int	getMin() This will give you the coordinate of the minimum point contained by this Location.
Location	intersection(Location l) Returns a Location that contains all points common to both ranges.
boolean	isContiguous() Delegates to the wrapped location.
boolean	overlaps(Location l) Checks if these two locations overlap, using this location's concept of overlapping.
boolean	overlapsOrigin() Does the Location overlap the origin (position 1) of the sequence?
SymbolList	symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
String	toString()
Location	union(Location l) Return a Location containing all points in either ranges.

Methods inherited from class org.biojava.bio.symbol.AbstractLocationDecorator

blockIterator, getDecorator, getWrapped, newInstance, translate

Methods inherited from class java.lang.Object

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

Constructor Detail

CircularLocation

public CircularLocation(Location wrapped,
                int length)

Constructs a CircularLocation by wrapping another Location It is preferable to use LocationTools to make CircularLocations

Parameters:

wrapped - the Location to wrap.

length - the length of the Sequence

CircularLocation

public CircularLocation(Location wrapped,
                int length,
                int fivePrimeEnd)

Makes a CircularLocation where the 5' end of the Location is specified. The fivePrimeEnd parameter must match one of the minimum coordinates of the wrapped Location. This allows the creation of Locations whose polarity can be specified. This method is used internally by LocationTools.union() and by the other constructor.

Parameters:

wrapped - the Location to map to a Circle

length - the lenght of the circle

fivePrimeEnd - the 5' polar end of the sequence

Throws:

IllegalArgumentException - if the 5' end doesn't match the min coordinate of either wrapped or one of its blocks.

Method Detail

getLength

public final int getLength()

overlapsOrigin

public boolean overlapsOrigin()

Does the Location overlap the origin (position 1) of the sequence?

If it does the Location will internally be composed of a CompoundLocation.

Returns:

true if it does, false otherwise

decorate

protected Location decorate(Location loc)

Specified by:

decorate in class AbstractLocationDecorator

contains

public boolean contains(int p)

Description copied from interface: Location

Checks if this location contains a point.

Specified by:

contains in interface Location

Overrides:

contains in class AbstractLocationDecorator

Parameters:

p - the point to check

Returns:

true if this contains p, otherwise false

intersection

public Location intersection(Location l)

Description copied from interface: Location

Returns a Location that contains all points common to both ranges.

Specified by:

intersection in interface Location

Overrides:

intersection in class AbstractLocationDecorator

Parameters:

l - the Location to intersect with

Returns:

a Location containing all points common to both, or the empty range if there are no such points

overlaps

public boolean overlaps(Location l)

Description copied from interface: Location

Checks if these two locations overlap, using this location's concept of overlapping.

Abstractly, two locations overlap if they both contain any point.

Specified by:

overlaps in interface Location

Overrides:

overlaps in class AbstractLocationDecorator

Parameters:

l - the Location to check

Returns:

true if they overlap, otherwise false

union

public Location union(Location l)

Description copied from interface: Location

Return a Location containing all points in either ranges.

Specified by:

union in interface Location

Overrides:

union in class AbstractLocationDecorator

Parameters:

l - the Location to union with

Returns:

a Location representing the union

contains

public boolean contains(Location l)

Description copied from interface: Location

Checks if this location contains the other.

Abstractly, a location contains another if every point in the other location is contained within this one.

Specified by:

contains in interface Location

Overrides:

contains in class AbstractLocationDecorator

Parameters:

l - the Location to check

Returns:

true if this contains l, otherwise false

equals

public boolean equals(Object o)

Description copied from interface: Location

Checks if this location is equivalent to the other.

Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location.

Specified by:

equals in interface Location

Overrides:

equals in class AbstractLocationDecorator

Parameters:

o - the Object to check

Returns:

true if this equals l, otherwise false

toString

public String toString()

Overrides:

toString in class Object

isContiguous

public boolean isContiguous()

Delegates to the wrapped location. Currently as locations that cross the origin are wrapped CompoundLocations they are not considered contiguous. This is desirable from the point of view of logical operations as it greatly simplifies the calculations of things such as contains, overlaps etc.

Specified by:

isContiguous in interface Location

Overrides:

isContiguous in class AbstractLocationDecorator

Returns:

true if the location is contiguous and doesn't overlap the origin

get5PrimeEnd

public int get5PrimeEnd()

The point at which indicates the 5' end of the Location. This is needed as compound circular locations have polarity. For example (18..30, 1..12) is not the same as (1..12, 18..30). The 5' coordinate is derived during construction of the Location. In particular during a union operation the 5' coordinate is generally the 5' coordinate of the first location in the union. In the case where this cannot be logically maintained the 5' coordinate will revert to getMin()

Returns:

the most 5' coordinate

See Also:

fivePrimeBlockIterator(), getMin(), get3PrimeEnd()

get3PrimeEnd

public int get3PrimeEnd()

Returns:

the most 3' coordinate

See Also:

fivePrimeBlockIterator(), getMax(), get5PrimeEnd()

getMin

public int getMin()

This will give you the coordinate of the minimum point contained by this Location. Generally this will be the leftmost end however if the Location crosses the origin then it will actually be the origin that is the minimum point and the method will return 1. If you want to be guarenteed of getting the leftmost coordinate then call get5PrimeEnd()

Specified by:

getMin in interface Location

Overrides:

getMin in class AbstractLocationDecorator

Returns:

the minimum coord

See Also:

get5PrimeEnd()

getMax

public int getMax()

This will give you the coordinate of the maximum point contained by this Location. Generally this will be the rightmost end however if the Location crosses the origin then it will actually be the point before the origin that is the maximum point and the method will return getLength(). If you want to be guarenteed of getting the rightmost coordinate then call get3PrimeEnd()

Specified by:

getMax in interface Location

Overrides:

getMax in class AbstractLocationDecorator

Returns:

the maximum coord

See Also:

get3PrimeEnd()

symbols

public SymbolList symbols(SymbolList seq)

Description copied from interface: Location

Return the symbols in a sequence that fall within this range.

Specified by:

symbols in interface Location

Overrides:

symbols in class AbstractLocationDecorator

Parameters:

seq - the SymbolList to process

Returns:

the SymbolList containing the symbols in seq in this range

fivePrimeBlockIterator

public ListIterator fivePrimeBlockIterator()

Iterates over the location blocks in order starting with the most 5'

Returns:

a ListIterator

See Also:

AbstractLocationDecorator.blockIterator(), get5PrimeEnd()