public interface Locatable
Modifier and Type | Method and Description |
---|---|
default boolean |
contains(Locatable other)
Determines whether this interval contains the entire region represented by other
(in other words, whether it covers it).
|
default boolean |
contigsMatch(Locatable other)
Determine if this is on the same contig as other
this must be equivalent to this.getContig().equals(other.getContig()) but may be implemented more efficiently
|
java.lang.String |
getContig()
Gets the contig name for the contig this is mapped to.
|
int |
getEnd() |
default int |
getLengthOnReference() |
int |
getStart() |
default boolean |
overlaps(Locatable other)
Determines whether this interval overlaps the provided locatable.
|
default boolean |
withinDistanceOf(Locatable other,
int distance)
Determines whether this interval comes within
distance of overlapping the provided locatable. |
java.lang.String getContig()
int getStart()
int getEnd()
default int getLengthOnReference()
default boolean overlaps(Locatable other)
other
- interval to checkdefault boolean withinDistanceOf(Locatable other, int distance)
distance
of overlapping the provided locatable.
When distance = 0 this is equal to overlaps(Locatable)
other
- interval to checkdistance
- how many bases may be between the two intervals for us to still consider them overlapping.default boolean contains(Locatable other)
other
- interval to checkdefault boolean contigsMatch(Locatable other)