Accessioned
, java.lang.Iterable<Location>
AccesionedLocation
AbstractLocation
, InsdcLocations.BondLocation
, InsdcLocations.GroupLocation
, InsdcLocations.OneOfLocation
, InsdcLocations.OrderLocation
, SequenceLocation
, SimpleLocation
public interface Location extends java.lang.Iterable<Location>, Accessioned
Modifier and Type | Interface | Description |
---|---|---|
static class |
Location.Tools |
Helper methods for use with the Location classes.
|
Modifier and Type | Field | Description |
---|---|---|
static Location |
EMPTY |
Basic location which is set to the minimum and maximum bounds of
Integer . |
Modifier and Type | Method | Description |
---|---|---|
Point |
getEnd() |
End of the location
|
int |
getLength() |
Returns the length of the outer bounds of this location
|
java.util.List<Location> |
getRelevantSubLocations() |
An extension to
getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations. |
<C extends Compound> |
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
|
java.util.List<Location> |
getSubLocations() |
Gives access to the sub locations for this location.
|
<C extends Compound> |
getSubSequence(Sequence<C> sequence) |
Will return a SequenceReader object which represents the outer bounds
of this Location
|
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.
|
getAccession
static final Location EMPTY
Integer
. Strand
is set to Strand.UNDEFINED
.Point getStart()
Point getEnd()
int getLength()
Strand getStrand()
java.util.List<Location> getSubLocations()
#getAllSubLocations()
.java.util.List<Location> getRelevantSubLocations()
getSubLocations()
which returns sub-locations
of sub-locations; this will continue until it runs out of those locations.boolean isComplex()
boolean isCircular()
boolean isBetweenCompounds()
<C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence)
sequence
- The sequence object to work with<C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)
sequence
- The sequence object to work with