FastqVariant (biojava 4.2.1 API)

java.lang.Object
- java.lang.Enum<FastqVariant>
- - org.biojava.nbio.sequencing.io.fastq.FastqVariant

All Implemented Interfaces:

Serializable, Comparable<FastqVariant>
```
public enum FastqVariant
extends Enum<FastqVariant>
```
FASTQ sequence format variant.

Since:

3.0.3

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

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`constrain(double qualityScore)` Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
`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.
`abstract int`	`qualityScore(double errorProbability)` Convert the specified error probability 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.
  - 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.
  - 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
  - qualityScore
```
public abstract int qualityScore(double errorProbability)
```
    Convert the specified error probability to a quality score.
    
    Parameters:
    
    errorProbability - error probability
    
    Returns:
    
    the specified error probability converted to a quality score
    
    Since:
    
    4.2
  - 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:
    
    3.0.6
  - 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
  - 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
  - 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
  - constrain
```
protected int constrain(double qualityScore)
```
    Constrain the specified quality score in double precision to the minimum and maximum quality scores in int precision.
    
    Parameters:
    
    qualityScore - quality score in double precision
    
    Returns:
    
    the specified quality score in double precision constrained to the minimum and maximum quality scores in int precision
    
    Since:
    
    4.2
  - 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

Enum FastqVariant

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

FASTQ_SANGER

FASTQ_SOLEXA

FASTQ_ILLUMINA

Method Detail

values

valueOf

getDescription

isSanger

isSolexa

isIllumina

minimumQualityScore

maximumQualityScore

qualityScore

qualityScore

quality

errorProbability

errorProbability

lowercaseName

constrain

parseFastqVariant