Package beagleutil

Class SampleIds

java.lang.Object

beagleutil.SampleIds

public final class SampleIds
extends java.lang.Object

Class SampleIds is a singleton class that represents a list of sample identifiers.

The singleton instance of SampleIds is thread-safe.

Method Summary

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

Returns the singleton SampleIds instance.

Returns:

the singleton SampleIds instance

getIndex

public int getIndex(java.lang.String id)

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

Parameters:

id - a sample identifier

Returns:

the index of the specified sample 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 sample identifier indices corresponding to the specified array of sample 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 sampled identifier, or returns -1 if the specified sample identifier is not indexed.

Parameters:

id - a sample identifiers

Returns:

the index of the specified sampled identifier, or -1 if the specified sample 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 sample identifiers.

Returns:

the number of indexed samples identifiers

id

public java.lang.String id(int index)

Returns the sample identifier with the specified index.

Parameters:

index - a sample identifier index

Returns:

the specified sample identifier

Throws:

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

ids

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

Returns a list of sample identifiers with the specified indices.

Parameters:

indices - an array of sample identifiers indices

Returns:

a list of sample identifiers with the specified indices

Throws:

java.lang.IndexOutOfBoundsException - if there exists a j satisfying (0 <= j && j < indices.length) && (indices[j] < 0 || indices[j] >= this.size())

ids

public java.lang.String[] ids()

Returns the list of indexed sample 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 && k < this.size().

Returns:

an array of sample 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