org.biojavax.bio.seq

Class RichLocation.Tools

java.lang.Object

org.biojavax.bio.seq.RichLocation.Tools

Enclosing interface:

RichLocation

public static class RichLocation.Tools
extends Object

Some useful tools for working with Locations.

Method Summary

Modifier and Type	Method and Description
static RichLocation	construct(Collection<Location> members) Constructs a RichLocation object based on the given collection of members.
static RichLocation	enrich(Location l) Attempts to convert a plain Location into a RichLocation.
static Collection<Location>	flatten(Collection<Location> members) Takes a set of locations and returns the set of all members.
static Collection<Location>	flatten(RichLocation location) Takes a location and returns the set of all members.
static boolean	isMultiSource(Collection<Location> members) Returns false if all the locations in the set are from the same strand of the same sequence.
static Collection<Location>	merge(Collection<Location> members) Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.
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.
static int[]	modulateCircularLocation(int start, int end, int seqLength) Takes a start and end position on a circular location of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.
static int[]	modulateCircularLocationPair(Location a, Location b, int seqLength) Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

construct

public static RichLocation construct(Collection<Location> members)

Constructs a RichLocation object based on the given collection of members. It the collection contains a single location, that is returned. If it contains multiple locations it returns a CompoundRichLocation covering them all, with the default term associated. It returns the empty location if the collection was empty.

Parameters:

members - the members to construct a location from.

Returns:

the corresponding RichLocation

isMultiSource

public static boolean isMultiSource(Collection<Location> members)

Returns false if all the locations in the set are from the same strand of the same sequence.

Parameters:

members - the set of locations to check.

Returns:

true if they are from multiple sources.

merge

public static Collection<Location> merge(Collection<Location> members)

Takes a set of locations and tries to merge all pairs where the union operation results in a simple rich location, not a compound one.

Parameters:

members - the members to merge

Returns:

the resulting merged set, which may have only one location in it.

flatten

public static Collection<Location> flatten(RichLocation location)

Takes a location and returns the set of all members. If any members are compound, it flattens them too.

Parameters:

location - the location to flatten

Returns:

the flattened collection of members.

flatten

public static Collection<Location> flatten(Collection<Location> members)

Takes a set of locations and returns the set of all members. If any members are compound, it flattens them too.

Parameters:

members - the locations to flatten

Returns:

the flattened collection of members.

modulateCircularLocation

public static int[] modulateCircularLocation(int start,
                                             int end,
                                             int seqLength)

Takes a start and end position on a circular location of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence.

Parameters:

start - the start of the circular location

end - the end of the circular location

seqLength - the circular length of the sequence underlying the location

Returns:

an integer array where [0] is the translated start and [1] the end.

modulateCircularLocationPair

public static int[] modulateCircularLocationPair(Location a,
                                                 Location b,
                                                 int seqLength)

Takes two circular locations of given length, and shifts them left along the sequence until they sit at the earliest possible point where they still would represent the same sequence. The end result ensures that simple overlap calculations will always work on the coordinates returned.

Parameters:

a - the first location to shift

b - the second location to shift

seqLength - the circular length of the sequence underlying the location

Returns:

an integer array where [0] is the translated start and [1] the end of location a, and [2] and [3] are the translated start and end of location b.

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 - the point on the location to shift

seqLength - the size of the circular location

Returns:

the shifted point

enrich

public static RichLocation enrich(Location l)

Attempts to convert a plain Location into a RichLocation.

Parameters:

l - the location to convert

Returns:

the converted location