Package org.biojava.bio.symbol

Class LocationTools

java.lang.Object
org.biojava.bio.symbol.LocationTools
public final class LocationTools extends Object
Tools class containing a number of operators for working with Location objects.

Most of the methods in this class are simple set-wise binary operators: for example, calculate the intersection of two locations.

This class provides helpful methods for set-wise manipulation of Location objects.
Since:
1.2
Author:
Matthew Pocock, Greg Cox, Thomas Down, Mark Schreiber, Francois Pepin

  • Method Details

    • union

      public static Location union(Location locA, Location locB)
      Return the union of two locations.

      The union will be a Location instance that contains every index contained by either locA or locB.

      Parameters:
      locA - the first Location
      locB - the second Location
      Returns:
      a Location that is the union of locA and locB

    • intersection

      public static Location intersection(Location locA, Location locB)
      Return the intersection of two locations.

      The intersection will be a Location instance that contains every index contained by both locA and locB.

      Parameters:
      locA - the first Location
      locB - the second Location
      Returns:
      a Location that is the intersection of locA and locB

    • canMerge

      public static boolean canMerge(Location locA, Location locB)
      Determines whether the locations are touching or not (if they could be merged in a single Location.

      Two locations can merge if they contain at least one index of one beside one index of the other.

      Parameters:
      locA - the first Location
      locB - the second Location
      Returns:
      true if they can merge, false otherwise

    • overlaps

      public static boolean overlaps(Location locA, Location locB)
      Determines whether the locations overlap or not.

      Two locations overlap if they contain at least one index in common.

      Parameters:
      locA - the first Location
      locB - the second Location
      Returns:
      true if they overlap, false otherwise

    • contains

      public static boolean contains(Location locA, Location locB)
      Return true iff all indices in locB are also contained by locA.
      Parameters:
      locA - The containing location
      locB - The contained location
      Returns:
      true is locA contains locB

    • areEqual

      public static boolean areEqual(Location locA, Location locB)
      Return whether two locations are equal.

      They are equal if both a contains b and b contains a. Equivalently, they are equal if for every point p, locA.contains(p) == locB.contains(p).

      Parameters:
      locA - the first Location
      locB - the second Location
      Returns:
      true if they are equivalent, false otherwise

    • union

      public static Location union(Collection locs)
      The n-way union of a Collection of locations. Returns a Location which covers every point covered by at least one of the locations in locs
      Parameters:
      locs - A collection of locations.
      Returns:
      A union location
      Throws:
      ClassCastException - if the collection contains non-Location objects.

    • makeLocation

      public static Location makeLocation(int min, int max)
      Return a contiguous Location from min to max.

      If min == max then a PointLocation will be made, otherwise, a RangeLocation will be returned.

      Parameters:
      min - the Location min value
      max - the Location max value
      Returns:
      a new Location from min to max

    • makeCircularLocation

      public static CircularLocation makeCircularLocation(int min, int max, int seqLength)
      A simple method to generate a RangeLocation wrapped in a CircularLocation. The method will cope with situtations where the min is greater than the max. Either of min or max can be negative, or greater than the underlying sequence length. If min and max are equal a wrapped point location will be made.
      Parameters:
      min - the "left" end of the location
      max - the "right" end of the location
      seqLength - the lenght of the sequence that the location will be applied to (for purposes of determining origin).
      Returns:
      the new CircularLocation

    • flip

      public static Location flip(Location loc, int len)
      Flips a location relative to a length.

      It is very common in biological sequences to represent locations on a sequence and then reverse that sequence. This method allows locations in the original coordinate space to be transformed int locations in the reverse one.

      Parameters:
      loc - the Location to flip
      len - the length of the region to flip within
      Returns:
      a flipped view of the location

    • subtract

      public static Location subtract(Location keep, Location remove)
      Subtract one location from another. This methods calculates the set of points which are contains in location keep but not in remove.
      Parameters:
      keep - A location
      remove - A location
      Returns:
      a location containing all points which are in x but not y
      Since:
      1.3

    • coverage

      public static int coverage(Location loc)
      Return the number of positions which are covered by a Location
      Parameters:
      loc - A location
      Returns:
      the number of distinct points contained by that location
      Since:
      1.4

    • shadow

      public static Location shadow(Location loc)
      Return a contiguous location running from the minimum to the maximum points of the specified location.
      Parameters:
      loc - a location
      Returns:
      a corresponding contiguous location

    • blockCount

      public static int blockCount(Location loc)
      Return the number of contiguous blocks in a location.
      Parameters:
      loc - a location
      Returns:
      the number of blocks
      Since:
      1.4