Uses of Class
com.milaboratory.core.sequence.SequenceQuality

Packages that use SequenceQuality

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.mutations
com.milaboratory.core.sequence
com.milaboratory.core.sequence.quality

Uses of SequenceQuality in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment with parameters of type SequenceQuality

Modifier and Type	Method and Description
MultiAlignmentHelper	MultiAlignmentHelper.addSubjectQuality(String title, SequenceQuality quality)
String	AlignmentHelper.toStringWithSeq2Quality(SequenceQuality quality)

Uses of SequenceQuality in com.milaboratory.core.mutations

Methods in com.milaboratory.core.mutations with parameters of type SequenceQuality

Modifier and Type	Method and Description
int	SequenceWeighter.getCoverageWeight(SequenceQuality quality, int position)
int	SequenceWeighter.getMutationWeight(SequenceQuality quality, int position, int mutation, int[] mutations)

Uses of SequenceQuality in com.milaboratory.core.sequence

Fields in com.milaboratory.core.sequence declared as SequenceQuality

Modifier and Type	Field and Description
static SequenceQuality	SequenceQuality.EMPTY

Methods in com.milaboratory.core.sequence that return SequenceQuality

Modifier and Type	Method and Description
SequenceQuality	SequenceQuality.concatenate(SequenceQuality... other)
static SequenceQuality	SequenceQuality.create(QualityFormat format, byte[] data, boolean check) Factory method for the SequenceQualityPhred object.
static SequenceQuality	SequenceQuality.create(QualityFormat format, byte[] data, int from, int length, boolean check) Factory method for the SequenceQualityPhred object.
SequenceQuality	SequenceWithQuality.getQuality() Returns quality.
SequenceQuality	SequenceQuality.getRange(int from, int to) Returns substring of current quality scores line.
SequenceQuality	SequenceQuality.getRange(Range range) Returns substring of current quality scores line.
static SequenceQuality	SequenceQuality.getUniformQuality(byte qualityValue, int length) Creates a phred sequence quality containing only given values of quality.
SequenceQuality	SequenceQuality.reverse() Gets quality values in reverse order

Methods in com.milaboratory.core.sequence with parameters of type SequenceQuality

Modifier and Type	Method and Description
SequenceQuality	SequenceQuality.concatenate(SequenceQuality... other)

Constructors in com.milaboratory.core.sequence with parameters of type SequenceQuality

Constructor and Description
NSequenceWithQuality(NucleotideSequence sequence, SequenceQuality quality) Creates nucleotide sequence with its quality
SequenceWithQuality(S sequence, SequenceQuality quality) Creates sequence with quality from specified values.

Uses of SequenceQuality in com.milaboratory.core.sequence.quality

Methods in com.milaboratory.core.sequence.quality that return SequenceQuality

Modifier and Type	Method and Description
SequenceQuality	SumQualityAggregator.getQuality()
SequenceQuality	QualityAggregator.getQuality()
SequenceQuality	MiniMaxQualityAggregator.getQuality()
SequenceQuality	MinimalQualityAggregator.getQuality()
SequenceQuality	MaximalQualityAggregator.getQuality()
SequenceQuality	AverageQualityAggregator.getQuality()

Methods in com.milaboratory.core.sequence.quality with parameters of type SequenceQuality

Modifier and Type	Method and Description
void	SumQualityAggregator.aggregate(SequenceQuality quality)
void	QualityAggregator.aggregate(SequenceQuality quality)
void	MiniMaxQualityAggregator.aggregate(SequenceQuality quality)
void	MinimalQualityAggregator.aggregate(SequenceQuality quality)
void	MaximalQualityAggregator.aggregate(SequenceQuality quality)
void	AverageQualityAggregator.aggregate(SequenceQuality quality)