public enum FastqVariant extends java.lang.Enum<FastqVariant>
Enum Constant | Description |
---|---|
FASTQ_ILLUMINA |
Illumina FASTQ sequence format variant.
|
FASTQ_SANGER |
Sanger FASTQ sequence format variant.
|
FASTQ_SOLEXA |
Solexa FASTQ sequence format variant.
|
Modifier and Type | Method | 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.
|
java.lang.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 . |
java.lang.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(java.lang.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(java.lang.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.
|
public static final FastqVariant FASTQ_SANGER
public static final FastqVariant FASTQ_SOLEXA
public static final FastqVariant FASTQ_ILLUMINA
public static FastqVariant[] values()
for (FastqVariant c : FastqVariant.values()) System.out.println(c);
public static FastqVariant valueOf(java.lang.String name)
name
- the name of the enum constant to be returned.java.lang.IllegalArgumentException
- if this enum type has no constant with the specified namejava.lang.NullPointerException
- if the argument is nullpublic java.lang.String getDescription()
public boolean isSanger()
FASTQ_SANGER
.FASTQ_SANGER
public boolean isSolexa()
FASTQ_SOLEXA
.FASTQ_SOLEXA
public boolean isIllumina()
FASTQ_ILLUMINA
.FASTQ_ILLUMINA
public abstract int minimumQualityScore()
public abstract int maximumQualityScore()
public abstract int qualityScore(char c)
c
- quality in ASCII formatpublic abstract int qualityScore(double errorProbability)
errorProbability
- error probabilitypublic abstract char quality(int qualityScore)
qualityScore
- quality score, must be >= minimumQualityScore()
and <= maximumQualityScore()
public double errorProbability(char c)
c
- quality in ASCII formatpublic abstract double errorProbability(int qualityScore)
qualityScore
- quality scorepublic java.lang.String lowercaseName()
lowercase-with-dashes
style.lowercase-with-dashes
styleprotected int constrain(double qualityScore)
qualityScore
- quality score in double precisionpublic static FastqVariant parseFastqVariant(java.lang.String name)
UPPERCASE_WITH_UNDERSCORES
or lowercase-with-dashes
style.name
- namenull
if no such FASTQ sequence format variant exists