Package 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
    Description
    Tools()
     

  • 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 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 Details

    • Tools

      public Tools()

  • Method Details

    • 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.