org.biojava.nbio.core.sequence.location.template

Class Location.Tools

java.lang.Object

org.biojava.nbio.core.sequence.location.template.Location.Tools

Enclosing interface:

Location

public static class Location.Tools
extends Object

Helper methods for use with the Location classes. Taking its inspiration from the RichSequence.Tools class from the old BioJava

Constructor Summary

Constructors

Constructor and Description
Tools()

Method Summary

Modifier and Type	Method and 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(List<Location> locations) Scans through a list of locations to find the Location with the highest end
static Location	getMin(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(List<Location> locations, Integer sequenceLength, 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Tools

public Tools()

Method Detail

location

public static Location location(List<Location> locations,
                                Integer sequenceLength,
                                String type)

Used for building a location from a series of sub-locations

location

public 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.

circularLocation

public 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. Unlike any other location builder this allows you to express your input location on the reverse strand

Parameters:

location - The location which currently expresses the outer bounds of a circular location.

length - The length of the circular genomic unit

Returns:

The circular location; can optionally return a normal non circular location if the one you give is within the bounds of the length

getMin

public static Location getMin(List<Location> locations)

Scans through a list of locations to find the Location with the lowest start

getMax

public static Location getMax(List<Location> locations)

Scans through a list of locations to find the Location with the highest end

modulateCircularIndex

public 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.

Parameters:

index - Index of the position to work with

seqLength - Length of the Sequence

Returns:

The shifted point

completeCircularPasses

public 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. 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.