Interface Location
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- All Superinterfaces:
Accessioned
,Iterable<Location>
- All Known Subinterfaces:
AccesionedLocation
- All Known Implementing Classes:
AbstractLocation
,InsdcLocations.BondLocation
,InsdcLocations.GroupLocation
,InsdcLocations.OneOfLocation
,InsdcLocations.OrderLocation
,SequenceLocation
,SimpleLocation
public interface Location extends Iterable<Location>, Accessioned
Sets of integers used to represent the location of features on sequence. A location can be a single set of bounds or composed of multiple sub-locations. Each sub-location is a Location and therefore subject to the same rules.- Author:
- ayates
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
Location.Tools
Helper methods for use with the Location classes.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Point
getEnd()
End of the locationint
getLength()
Returns the length of the outer bounds of this locationList<Location>
getRelevantSubLocations()
An extension togetSubLocations()
which returns sub-locations of sub-locations; this will continue until it runs out of those locations.<C extends Compound>
Sequence<C>getRelevantSubSequence(Sequence<C> sequence)
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 representedPoint
getStart()
Start of the locationStrand
getStrand()
Strand which the location is located onList<Location>
getSubLocations()
Gives access to the sub locations for this location.<C extends Compound>
Sequence<C>getSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which represents the outer bounds of this Locationboolean
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.-
Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned
getAccession
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Methods inherited from interface java.lang.Iterable
forEach, iterator, spliterator
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Field Detail
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EMPTY
static final Location EMPTY
Basic location which is set to the minimum and maximum bounds ofInteger
.Strand
is set toStrand.UNDEFINED
.
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Method Detail
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getLength
int getLength()
Returns the length of the outer bounds of this location
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getSubLocations
List<Location> getSubLocations()
Gives access to the sub locations for this location. However this does not return sub-locations of sub-locations. For that functionality use#getAllSubLocations()
.- Returns:
- A list of a single level of sub-locations
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getRelevantSubLocations
List<Location> getRelevantSubLocations()
An extension togetSubLocations()
which returns sub-locations of sub-locations; this will continue until it runs out of those locations.- Returns:
- List of all sub locations including sub-locations of sub locations
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isComplex
boolean isComplex()
Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
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isCircular
boolean isCircular()
Indicates if this location is circular.
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isBetweenCompounds
boolean isBetweenCompounds()
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.
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getSubSequence
<C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which represents the outer bounds of this Location- Parameters:
sequence
- The sequence object to work with- Returns:
- The sequence
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getRelevantSubSequence
<C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)
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- Parameters:
sequence
- The sequence object to work with- Returns:
- The full assembled sequence
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