Class 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

      All Methods Static Methods Concrete Methods 
      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. 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 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.
    • Constructor Detail

    • Method Detail

      • 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.