public final class LocationTools extends Object
Location
objects.
Most of the methods in this class are simple setwise binary operators: for example, calculate the intersection of two locations.
This class provides helpful methods for setwise manipulation of Location objects.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 nway union of a Collection of locations.

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

public static Location union(Location locA, Location locB)
The union will be a Location instance that contains every index contained by either locA or locB.
locA
 the first LocationlocB
 the second Locationpublic static Location intersection(Location locA, Location locB)
The intersection will be a Location instance that contains every index contained by both locA and locB.
locA
 the first LocationlocB
 the second Locationpublic static boolean canMerge(Location locA, Location locB)
Two locations can merge if they contain at least one index of one beside one index of the other.
locA
 the first LocationlocB
 the second Locationtrue
if they can merge, false
otherwisepublic static boolean overlaps(Location locA, Location locB)
Two locations overlap if they contain at least one index in common.
locA
 the first LocationlocB
 the second Locationtrue
if they overlap, false
otherwisepublic static boolean contains(Location locA, Location locB)
true
iff all indices in locB
are also contained
by locA
.locA
 The containing locationlocB
 The contained locationtrue
is locA contains locBpublic static boolean areEqual(Location locA, Location locB)
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).
locA
 the first LocationlocB
 the second Locationpublic static Location union(Collection locs)
locs
locs
 A collection of locations.ClassCastException
 if the collection contains nonLocation objects.public static Location makeLocation(int min, int max)
If min == max then a PointLocation will be made, otherwise, a RangeLocation will be returned.
min
 the Location min valuemax
 the Location max valuepublic static CircularLocation makeCircularLocation(int min, int max, int seqLength)
min
 the "left" end of the locationmax
 the "right" end of the locationseqLength
 the lenght of the sequence that the location will
be applied to (for purposes of determining origin).CircularLocation
public static Location flip(Location loc, int len)
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.
loc
 the Location to fliplen
 the length of the region to flip withinpublic static Location subtract(Location keep, Location remove)
keep
but not in
remove
.keep
 A locationremove
 A locationpublic static int coverage(Location loc)
Location
loc
 A locationpublic static Location shadow(Location loc)
loc
 a locationpublic static int blockCount(Location loc)
loc
 a locationCopyright © 2014 BioJava. All rights reserved.