org.broadinstitute.hellbender.utils

Class Nucleotide.Counter

java.lang.Object

org.broadinstitute.hellbender.utils.Nucleotide.Counter

Enclosing class:

Nucleotide

public static final class Nucleotide.Counter
extends java.lang.Object

Helper class to count the number of occurrences of each nucleotide code in a sequence.

Constructor Summary

Constructors

Constructor and Description
Counter() Creates a new counter with all counts set to 0.

Method Summary

Modifier and Type	Method and Description
void	add(byte base) Increases the nucleotide that corresponds to the input base own count by 1.
void	add(char base)
void	add(Nucleotide nucleotide) Increases by 1 the count for a nucleotide.
void	addAll(byte... bases) Increase by one the count for a nucleotide for each occurrence of such in the input byte array base codes.
void	addAll(char... bases) Increase by one the count for a nucleotide for each occurrence of such in the input char array base codes.
void	addAll(java.lang.CharSequence bases) Increase by one the count for a nucleotide for each occurrence of such in the input CharSequence.
void	clear() Reset all the counts to 0.
long	get(Nucleotide nucleotide) Returns the current count for a given nucleotide.
long	sum() Return the total count of all nucleotide constants.

Methods inherited from class java.lang.Object

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

Constructor Detail

Counter

public Counter()

Creates a new counter with all counts set to 0.

Method Detail

add

public void add(Nucleotide nucleotide)

Increases by 1 the count for a nucleotide.

Parameters:

nucleotide - the target nucleotide.

Throws:

java.lang.IllegalArgumentException - if nucleotide is null.

add

public void add(byte base)

Increases the nucleotide that corresponds to the input base own count by 1.

Parameters:

base - the base code.

Throws:

java.lang.IllegalArgumentException - if base is negative.

add

public void add(char base)

get

public long get(Nucleotide nucleotide)

Returns the current count for a given nucleotide.

Parameters:

nucleotide - the query nucleotide.

Returns:

0 or greater.

Throws:

java.lang.IllegalArgumentException - if nucleotide is null.

addAll

public final void addAll(byte... bases)

Increase by one the count for a nucleotide for each occurrence of such in the input byte array base codes.

Parameters:

bases - the input base codes.

Throws:

java.lang.IllegalArgumentException - if bases is null.

addAll

public final void addAll(char... bases)

Increase by one the count for a nucleotide for each occurrence of such in the input char array base codes.

Parameters:

bases - the input base codes.

Throws:

java.lang.IllegalArgumentException - if bases is null.

addAll

public final void addAll(java.lang.CharSequence bases)

Increase by one the count for a nucleotide for each occurrence of such in the input CharSequence.

Parameters:

bases - the input bases sequence.

Throws:

java.lang.IllegalArgumentException - if the input is null.

clear

public void clear()

Reset all the counts to 0.

sum

public long sum()

Return the total count of all nucleotide constants.

Returns:

0 or greater.