public static class Location.Tools
extends java.lang.Object
Constructor | Description |
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Tools() |
Modifier and Type | Method | Description |
---|---|---|
static Location |
circularLocation(int start,
int end,
Strand strand,
int length) |
Converts a location which defines the outer bounds of a circular
location and splits it into the required portions.
|
static int |
completeCircularPasses(int index,
int seqLength) |
Works in a similar way to modulateCircularLocation but returns
the number of complete passes over a Sequence length a circular
location makes i.e.
|
static Location |
getMax(java.util.List<Location> locations) |
Scans through a list of locations to find the Location with the
highest end
|
static Location |
getMin(java.util.List<Location> locations) |
Scans through a list of locations to find the Location with the
lowest start
|
static Location |
location(int start,
int end,
Strand strand,
int length) |
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.
|
static Location |
location(java.util.List<Location> locations,
java.lang.Integer sequenceLength,
java.lang.String type) |
Used for building a location from a series of sub-locations
|
static int |
modulateCircularIndex(int index,
int seqLength) |
Takes a point on a circular location and moves it left until it falls
at the earliest possible point that represents the same base.
|
public static Location location(java.util.List<Location> locations, java.lang.Integer sequenceLength, java.lang.String type)
public static Location location(int start, int end, Strand strand, int length)
public static Location circularLocation(int start, int end, Strand strand, int length)
location
- The location which currently expresses the outer
bounds of a circular location.length
- The length of the circular genomic unitpublic static Location getMin(java.util.List<Location> locations)
public static Location getMax(java.util.List<Location> locations)
public static int modulateCircularIndex(int index, int seqLength)
index
- Index of the position to work withseqLength
- Length of the Sequencepublic static int completeCircularPasses(int index, int seqLength)