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 Summary

Methods

Modifier and Type	Method and Description
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