Uses of Class artificialFastqGenerator.Nucleobase
Date: 2014-10-01

## Uses of Class
artificialFastqGenerator.Nucleobase

- - ### Uses of Nucleobase in artificialFastqGenerator

    Methods in artificialFastqGenerator that return Nucleobase
    Modifier and Type | Method and Description
    --- | ---
    `Nucleobase` | NucleobaseAndReadFactory.`createNucleobase(char genotype)` Create a Nucleobase object.

    Methods in artificialFastqGenerator that return types with arguments of type Nucleobase
    Modifier and Type | Method and Description
    --- | ---
    `java.util.ArrayList<Nucleobase>` | AbstractRead.`getSequence()` Return the sequence of nucleobases from the reference genome which this Read object is a read of.

    Methods in artificialFastqGenerator with parameters of type Nucleobase
    Modifier and Type | Method and Description
    --- | ---
    `void` | CoverageStatisticsCalculator.`updateRegionStatsFrom1Nucleobase(Nucleobase nucleobase)` Update the region coverage statistics from the coverage statistics for 1 nucleobase in that region.

    Method parameters in artificialFastqGenerator with type arguments of type Nucleobase
    Modifier and Type | Method and Description
    --- | ---
    `void` | NucleobaseAndReadFactory.`createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence, java.util.ArrayList<Nucleobase> rightEndSequence)` Create a pair of reads.
    `void` | NucleobaseAndReadFactory.`createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence, java.util.ArrayList<Nucleobase> rightEndSequence)` Create a pair of reads.
    `java.util.ArrayList<char[]>` | QualityScoreAndErrorGenerator.`getQualityScoresAndGenotypesRead(boolean isLeft, java.util.ArrayList<Nucleobase> nucleobases)` Get the encoded phred quality scores and the genotypes read.
    `void` | AbstractRead.`setSequence(java.util.ArrayList<Nucleobase> sequence)` Set the sequence of nucleobases from the reference genome which this Read object is a read of.

    Constructor parameters in artificialFastqGenerator with type arguments of type Nucleobase
    Constructor and Description
    `Read(java.util.ArrayList<Nucleobase> sequence, long uniqueID, Read pairedEndRead, boolean leftPEAndNeedsWriting, char[] encodedQualityScores, char[] genotypesThatAreRead, int xCoordinate, int yCoordinate)` Initialise a new Read object.