beagleutil

Class Samples

java.lang.Object

beagleutil.Samples

public final class Samples
extends java.lang.Object

Class Samples stores a list of samples.

Instances of class Samples are immutable.

Constructor Summary

Constructors

Constructor and Description
Samples(int[] idIndices) Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj) Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
static Samples	fromIds(java.lang.String[] ids) Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
int	hashCode() Returns a hash code value for the object.
java.lang.String	id(int index) Returns the identifier for the sample with the specified index in this list of samples.
int	idIndex(int index) Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
java.lang.String[]	ids() Returns this list of samples as an array of sample identifiers.
int	index(int idIndex) Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.
int	index(java.lang.String id) Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.
int	nSamples() Returns the number of samples in this list.
java.lang.String	toString() Returns java.util.Arrays.toString(this.ids()).

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Samples

public Samples(int[] idIndices)

Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.

Parameters:

idIndices - an array of sample identifier indices

Throws:

java.lang.IllegalArgumentException - if the specified array has two or more elements that are equal

java.lang.IndexOutOfBoundsException - if any element of the specified array is negative or greater than or equal to beagleutil.SampleIds.size()

java.lang.NullPointerException - if idIndices == null

Method Detail

fromIds

public static Samples fromIds(java.lang.String[] ids)

Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.

Parameters:

ids - an array of sample identifiers.

Returns:

a Samples instance corresponding to the specified list of sample identifiers

Throws:

java.lang.IllegalArgumentException - if the specified array has two or more elements that are equal as strings

java.lang.NullPointerException - if ids == null

hashCode

public int hashCode()

Returns a hash code value for the object.

The hash code is defined by the following calculation:

        int hash = 1;
        for (int j, n=this.nSamples(); j<n; ++j) {
            hash = 31 * hash + this.idIndex(j);
        }
 

Overrides:

hashCode in class java.lang.Object

Returns:

a hash code value for the object.

equals

public boolean equals(java.lang.Object obj)

Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.

Overrides:

equals in class java.lang.Object

Parameters:

obj - the object to be tested for equality with this

Returns:

true if the specified object is a Samples object which represents the same ordered list of samples as this

idIndex

public int idIndex(int index)

Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.

Parameters:

index - a sample index

Returns:

the sample identifier index corresponding to the sample with the specified index in this list of samples

Throws:

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

index

public int index(int idIndex)

Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.

Parameters:

idIndex - a sample identifier index

Returns:

the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples

Throws:

java.lang.IndexOutOfBoundsException - if index < 0

index

public int index(java.lang.String id)

Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.

Parameters:

id - a sample identifier

Returns:

the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples

Throws:

java.lang.NullPointerException - if id == null

nSamples

public int nSamples()

Returns the number of samples in this list.

Returns:

the number of samples in this list

id

public java.lang.String id(int index)

Returns the identifier for the sample with the specified index in this list of samples.

Parameters:

index - a sample index

Returns:

the identifier for the sample with the specified index in this list of samples

Throws:

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

ids

public java.lang.String[] ids()

Returns this list of samples as an array of sample identifiers. The returned array has length this.nSamples(), and it satisfies this.ids()[j].equals(this.id(j)) for 0 <= j && j < this.nSamples()

Returns:

this list of samples as 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