Package beagleutil

Class ChromIds

java.lang.Object

beagleutil.ChromIds

public final class ChromIds
extends java.lang.Object

Class ChromIds is a singleton class that represents a list of chromosome identifiers.

The singleton instance of ChromIds is thread-safe.

Method Summary

Modifier and Type	Method	Description
int	getIndex(java.lang.String id)	Returns the index of the specified chromosome identifier.
int	getIndexIfIndexed(java.lang.String id)	Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.
int[]	getIndices(java.lang.String[] ids)	Returns an array of chromosome identifier indices corresponding to the specified array of chromosome identifiers.
java.lang.String	id(int index)	Returns the chromosome identifier with the specified index.
java.lang.String[]	ids()	Returns the list of chromosome identifiers as an array.
static ChromIds	instance()	Returns the singleton ChromIds instance.
int	size()	Returns the number of indexed chromosomes identifiers.
java.lang.String	toString()	Returns java.util.Arrays.toString(this.ids()).

Methods inherited from class java.lang.Object

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

Method Detail

instance

public static ChromIds instance()

Returns the singleton ChromIds instance.

Returns:

the singleton ChromIds instance

getIndex

public int getIndex(java.lang.String id)

Returns the index of the specified chromosome identifier. If the chromosome identifiers is not yet indexed, the chromosome identifier will be indexed. Chromosome identifier indices are assigned in consecutive order beginning with 0.

Parameters:

id - a chromosome identifier

Returns:

the index of the specified chromosome identifier

Throws:

java.lang.IllegalArgumentException - if id.isEmpty()

java.lang.NullPointerException - if id == null

getIndices

public int[] getIndices(java.lang.String[] ids)

Returns an array of chromosome identifier indices corresponding to the specified array of chromosome identifiers. If a sample identifier is not yet indexed, the sample identifier will be indexed. Sample identifier indices are assigned in increasing order starting with 0.

Parameters:

ids - an array of sample identifiers

Returns:

an array of sample identifier indices

Throws:

java.lang.IllegalArgumentException - if there is a j satisfying (0 <= j && j < ids.length) && ids[j].isEmpty()

java.lang.NullPointerException - if ids == null

java.lang.NullPointerException - if there is a j satisfying (0 <= j && j < ids.length) && (ids[j] == null)

getIndexIfIndexed

public int getIndexIfIndexed(java.lang.String id)

Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.

Parameters:

id - a chromosome identifier.

Returns:

the index of the specified chromosome identifier, or -1 if the specified chromosome identifier is not indexed.

Throws:

java.lang.IllegalArgumentException - if id.isEmpty()

java.lang.NullPointerException - if id == null

size

public int size()

Returns the number of indexed chromosomes identifiers.

Returns:

the number of indexed chromosomes identifiers

id

public java.lang.String id(int index)

Returns the chromosome identifier with the specified index.

Parameters:

index - a chromosome identifier index.

Returns:

the specified chromosome identifier.

Throws:

java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.size()

ids

public java.lang.String[] ids()

Returns the list of chromosome identifiers as an array. The returned array will have length this.size(), and it will satisfy this.ids()[k].equals(this.id(k)) == true for 0 <= k < this.size().

Returns:

an array of chromosome identifiers

toString

public java.lang.String toString()

Returns java.util.Arrays.toString(this.ids()).

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this