Used for building a location from a series of sub-locations
public static Location location(int start,
Returns a location object which unlike the location constructors
allows you to input reverse coordinates and will convert
these into the right location on the positive strand.
public static Location circularLocation(int start,
Converts a location which defines the outer bounds of a circular
location and splits it into the required portions. Unlike any
other location builder this allows you to express your input
location on the reverse strand
location - The location which currently expresses the outer
bounds of a circular location.
length - The length of the circular genomic unit
The circular location; can optionally return a normal non
circular location if the one you give is within the bounds of
Scans through a list of locations to find the Location with the
public static int modulateCircularIndex(int index,
Takes a point on a circular location and moves it left until it falls
at the earliest possible point that represents the same base.
index - Index of the position to work with
seqLength - Length of the Sequence
The shifted point
public static int completeCircularPasses(int index,
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e. if we have a sequence of length 10 and the
location 3..52 we make 4 complete passes through the genome to
go from position 3 to position 52.