org.biojava.bio.symbol
Class LocationTools

java.lang.Object
  extended by 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.

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

Method Summary
static boolean areEqual(Location locA, Location locB)
          Return whether two locations are equal.
static int blockCount(Location loc)
          Return the number of contiguous blocks in a location.
static boolean canMerge(Location locA, Location locB)
          Determines whether the locations are touching or not (if they could be merged in a single Location.
static boolean contains(Location locA, Location locB)
          Return true iff all indices in locB are also contained by locA.
static int coverage(Location loc)
          Return the number of positions which are covered by a Location
static Location flip(Location loc, int len)
          Flips a location relative to a length.
static Location intersection(Location locA, Location locB)
          Return the intersection of two locations.
static CircularLocation makeCircularLocation(int min, int max, int seqLength)
          A simple method to generate a RangeLocation wrapped in a CircularLocation.
static Location makeLocation(int min, int max)
          Return a contiguous Location from min to max.
static boolean overlaps(Location locA, Location locB)
          Determines whether the locations overlap or not.
static Location shadow(Location loc)
          Return a contiguous location running from the minimum to the maximum points of the specified location.
static Location subtract(Location keep, Location remove)
          Subtract one location from another.
static Location union(Collection locs)
          The n-way union of a Collection of locations.
static Location union(Location locA, Location locB)
          Return the union of two locations.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

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