org.biojava.nbio.core.sequence.location

Class LocationHelper

java.lang.Object

org.biojava.nbio.core.sequence.location.LocationHelper

public class LocationHelper
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
LocationHelper()

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. 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.
static boolean	consistentAccessions(List<Location> subLocations) Scans a list of locations and returns true if all the given locations are linked to the same sequence.
static boolean	detectCicular(List<Location> subLocations) Loops through the given list of locations and returns true if it looks like they represent a circular location.
static Point	detectEnd(List<Location> subLocations, boolean isCircular) This will attempt to find what the last point is and returns that position.
static Point	detectStart(List<Location> subLocations) Assumes that the first element is the start & clones it
static Strand	detectStrand(List<Location> subLocations) Loops through the given list of locations and returns the consensus Strand class.
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> subLocations) Used as a thin wrapper to the location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
static Location	location(List<Location> subLocations, String type) Builds a location from a List of locations; this can be circular or linear joins.
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

LocationHelper

public LocationHelper()

Method Detail

location

public static Location location(List<Location> subLocations)

Used as a thin wrapper to the location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)

location

public static Location location(List<Location> subLocations,
                                String type)

Builds a location from a List of locations; this can be circular or linear joins. The code expects that these locations are in a sensible format.

Parameters:

subLocations - The list of locations to use to build the location. If given a list of size 1 we will return that location.

type - The type of join for this location; defaults to join

Returns:

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.

detectCicular

public static boolean detectCicular(List<Location> subLocations)

Loops through the given list of locations and returns true if it looks like they represent a circular location. Detection cannot happen if we do not have consistent accessions

consistentAccessions

public static boolean consistentAccessions(List<Location> subLocations)

Scans a list of locations and returns true if all the given locations are linked to the same sequence. A list of null accessioned locations is the same as a list where the accession is the same

Parameters:

subLocations - The locations to scan

Returns:

Returns a boolean indicating if this is consistently accessioned

detectStrand

public static Strand detectStrand(List<Location> subLocations)

Loops through the given list of locations and returns the consensus Strand class. If the class switches then we will return an undefined strand

detectStart

public static Point detectStart(List<Location> subLocations)

Assumes that the first element is the start & clones it

detectEnd

public static Point detectEnd(List<Location> subLocations,
                              boolean isCircular)

This will attempt to find what the last point is and returns that position. If the location is circular this will return the total length of the location and does not mean the maximum point on the Sequence we may find the locations on