org.biojava.bio.program.fastq

Enum FastqVariant

java.lang.Object

java.lang.Enum<FastqVariant>

org.biojava.bio.program.fastq.FastqVariant

All Implemented Interfaces:

Serializable, Comparable<FastqVariant>

public enum FastqVariant
extends Enum<FastqVariant>

FASTQ sequence format variant.

Since:

1.7.1

Enum Constant Summary

Enum Constants

Enum Constant and Description
FASTQ_ILLUMINA Illumina FASTQ sequence format variant.
FASTQ_SANGER Sanger FASTQ sequence format variant.
FASTQ_SOLEXA Solexa FASTQ sequence format variant.

Method Summary

Methods

Modifier and Type	Method and Description
double	errorProbability(char c) Convert the specified quality in ASCII format to an error probability.
abstract double	errorProbability(int qualityScore) Calculate the error probability given the specified quality score.
String	getDescription() Return the description of this FASTQ sequence format variant.
boolean	isIllumina() Return true if this FASTQ sequence format variant is FASTQ_ILLUMINA.
boolean	isSanger() Return true if this FASTQ sequence format variant is FASTQ_SANGER.
boolean	isSolexa() Return true if this FASTQ sequence format variant is FASTQ_SOLEXA.
String	lowercaseName() Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.
abstract int	maximumQualityScore() Return the maximum quality score for this FASTQ sequence format variant.
abstract int	minimumQualityScore() Return the minimum quality score for this FASTQ sequence format variant.
static FastqVariant	parseFastqVariant(String name) Return the FASTQ sequence format variant with the specified name, if any.
abstract char	quality(int qualityScore) Convert the specified quality score to a quality in ASCII format.
abstract int	qualityScore(char c) Convert the specified quality in ASCII format to a quality score.
static FastqVariant	valueOf(String name) Returns the enum constant of this type with the specified name.
static FastqVariant[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

FASTQ_SANGER

public static final FastqVariant FASTQ_SANGER

Sanger FASTQ sequence format variant.

FASTQ_SOLEXA

public static final FastqVariant FASTQ_SOLEXA

Solexa FASTQ sequence format variant.

FASTQ_ILLUMINA

public static final FastqVariant FASTQ_ILLUMINA

Illumina FASTQ sequence format variant.

Method Detail

values

public static FastqVariant[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (FastqVariant c : FastqVariant.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static FastqVariant valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getDescription

public String getDescription()

Return the description of this FASTQ sequence format variant. The description will not be null.

Returns:

the description of this FASTQ sequence format variant

isSanger

public boolean isSanger()

Return true if this FASTQ sequence format variant is FASTQ_SANGER.

Returns:

true if this FASTQ sequence format variant is FASTQ_SANGER

isSolexa

public boolean isSolexa()

Return true if this FASTQ sequence format variant is FASTQ_SOLEXA.

Returns:

true if this FASTQ sequence format variant is FASTQ_SOLEXA

isIllumina

public boolean isIllumina()

Return true if this FASTQ sequence format variant is FASTQ_ILLUMINA.

Returns:

true if this FASTQ sequence format variant is FASTQ_ILLUMINA

minimumQualityScore

public abstract int minimumQualityScore()

Return the minimum quality score for this FASTQ sequence format variant.

Returns:

the minimum quality score for this FASTQ sequence format variant.

Since:

1.8.2

maximumQualityScore

public abstract int maximumQualityScore()

Return the maximum quality score for this FASTQ sequence format variant.

Returns:

the maximum quality score for this FASTQ sequence format variant.

Since:

1.8.2

qualityScore

public abstract int qualityScore(char c)

Convert the specified quality in ASCII format to a quality score.

Parameters:

c - quality in ASCII format

Returns:

the specified quality in ASCII format converted to a quality score

Since:

1.8.2

quality

public abstract char quality(int qualityScore)

Convert the specified quality score to a quality in ASCII format.

Parameters:

qualityScore - quality score, must be >= minimumQualityScore() and <= maximumQualityScore()

Returns:

the quality in ASCII format converted from the specified quality score

Since:

1.8.3

errorProbability

public double errorProbability(char c)

Convert the specified quality in ASCII format to an error probability.

Parameters:

c - quality in ASCII format

Returns:

the specified quality in ASCII format converted to an error probability

Since:

1.8.2

errorProbability

public abstract double errorProbability(int qualityScore)

Calculate the error probability given the specified quality score.

Parameters:

qualityScore - quality score

Returns:

the error probability given the specified quality score

Since:

1.8.2

lowercaseName

public String lowercaseName()

Return the name of this FASTQ sequence format variant in lowercase-with-dashes style.

Returns:

the name of this FASTQ sequence format variant in lowercase-with-dashes style

parseFastqVariant

public static FastqVariant parseFastqVariant(String name)

Return the FASTQ sequence format variant with the specified name, if any. The name may be specified in either UPPERCASE_WITH_UNDERSCORES or lowercase-with-dashes style.

Parameters:

name - name

Returns:

the FASTQ sequence format variant with the specified name, or null if no such FASTQ sequence format variant exists