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

Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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




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. ThefivePrimeEnd
parameter must match one of the minimum coordinates of the wrappedLocation
. This allows the creation of Locations whose polarity can be specified. This method is used internally byLocationTools.union()
and by the other constructor. Parameters:
wrapped
 theLocation
to map to a Circlelength
 the lenght of the circlefivePrimeEnd
 the 5' polar end of the sequence Throws:
IllegalArgumentException
 if the 5' end doesn't match the min coordinate of eitherwrapped
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 classAbstractLocationDecorator

contains
public boolean contains(int p)
Description copied from interface:Location
Checks if this location contains a point. Specified by:
contains
in interfaceLocation
 Overrides:
contains
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
intersection
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
overlaps
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
union
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
contains
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
equals
in classAbstractLocationDecorator
 Parameters:
o
 the Object to check Returns:
 true if this equals l, otherwise false

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 interfaceLocation
 Overrides:
isContiguous
in classAbstractLocationDecorator
 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 togetMin()
 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 callget5PrimeEnd()
 Specified by:
getMin
in interfaceLocation
 Overrides:
getMin
in classAbstractLocationDecorator
 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 returngetLength()
. If you want to be guarenteed of getting the rightmost coordinate then callget3PrimeEnd()
 Specified by:
getMax
in interfaceLocation
 Overrides:
getMax
in classAbstractLocationDecorator
 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 interfaceLocation
 Overrides:
symbols
in classAbstractLocationDecorator
 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()

