Uses of Class
org.snpeff.binseq.DnaSequence

Packages that use DnaSequence

Package	Description
org.snpeff.binseq
org.snpeff.binseq.comparator
org.snpeff.interval
org.snpeff.overlap

Uses of DnaSequence in org.snpeff.binseq

Subclasses of DnaSequence in org.snpeff.binseq

Modifier and Type	Class	Description
class	DnaNSequence	Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
class	DnaSequenceId	Binary packed DNA sequence with an ID (long)

Methods in org.snpeff.binseq that return DnaSequence

Modifier and Type	Method	Description
DnaSequence	DnaSequence.clone()
static DnaSequence	DnaSequence.empty()	Empty sequence singleton
protected DnaSequence	DnaSequence.factory()	Create a new sequence
protected DnaSequence	DnaSequenceId.factory()	Create sequences
DnaSequence	DnaSequencePe.getSeq1()
DnaSequence	DnaSequencePe.getSeq2()

Uses of DnaSequence in org.snpeff.binseq.comparator

Classes in org.snpeff.binseq.comparator with type parameters of type DnaSequence

Modifier and Type	Class	Description
class	DnaSubsequenceComparator<T extends DnaSequence>	Compares two subsequences of DNA (DnaSequence)

Methods in org.snpeff.binseq.comparator with parameters of type DnaSequence

Modifier and Type	Method	Description
int	DnaSubsequenceComparator.compare(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
int	DnaSubsequenceComparator.score(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
int	DnaSubsequenceComparator.scoreSlow(DnaSequence seq1, int index1, DnaSequence seq2, int index2)	This method is used when none of the indexes is zero.

Uses of DnaSequence in org.snpeff.interval

Methods in org.snpeff.interval that return DnaSequence

Modifier and Type	Method	Description
DnaSequence	Chromosome.getDnaSequence()

Uses of DnaSequence in org.snpeff.overlap

Methods in org.snpeff.overlap that return DnaSequence

Modifier and Type	Method	Description
DnaSequence	SequenceRotator.calcRor(int rotate)
DnaSequence	SequenceRotator.rotate(int rotate)	Rotate left

Methods in org.snpeff.overlap with parameters of type DnaSequence

Modifier and Type	Method	Description
int	OverlapDnaSeq.overlap(DnaSequence seq1, DnaSequence seq2)

Constructors in org.snpeff.overlap with parameters of type DnaSequence

Constructor	Description
SequenceRotator(DnaSequence sequence)