Package 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
    Description
    LocationHelper()
     

  • Method Summary

    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 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 Details

    • LocationHelper

      public LocationHelper()

  • Method Details

    • 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