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public interface Location
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.
Nested Class Summary | |
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static class |
Location.Tools
Helper methods for use with the Location classes. |
Field Summary | |
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static Location |
EMPTY
Basic location which is set to the minimum and maximum bounds of Integer . |
Method Summary | ||
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Point |
getEnd()
End of the location |
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int |
getLength()
Returns the length of the outer bounds of this location |
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List<Location> |
getRelevantSubLocations()
An extension to getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations. |
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getRelevantSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which offers a view of all resolved locations i.e. |
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Point |
getStart()
Start of the location |
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Strand |
getStrand()
Strand which the location is located on |
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List<Location> |
getSubLocations()
Gives access to the sub locations for this location. |
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getSubSequence(Sequence<C> sequence)
Will return a SequenceReader object which represents the outer bounds of this Location |
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boolean |
isBetweenCompounds()
Returns true if the position is meant to represent a point between two points such as 78^79. |
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boolean |
isCircular()
Indicates if this location is circular. |
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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 java.lang.Iterable |
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iterator |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
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getAccession |
Field Detail |
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static final Location EMPTY
Integer
. Strand
is set to Strand.UNDEFINED
.
Method Detail |
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Point getStart()
Point getEnd()
int getLength()
Strand getStrand()
List<Location> getSubLocations()
#getAllSubLocations()
.
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)
<C>
- The type of compound to usesequence
- The sequence object to work with
<C extends Compound> Sequence<C> getRelevantSubSequence(Sequence<C> sequence)
<C>
- The type of compound to usesequence
- The sequence object to work with
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