Uses of Class
org.snpeff.binseq.DnaSequence
Packages that use DnaSequence
Package
Description
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Uses of DnaSequence in org.snpeff.binseq
Subclasses of DnaSequence in org.snpeff.binseqModifier and TypeClassDescriptionclass
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}class
Binary packed DNA sequence with an ID (long)Methods in org.snpeff.binseq that return DnaSequenceModifier and TypeMethodDescriptionDnaSequence.clone()
static DnaSequence
DnaSequence.empty()
Empty sequence singletonprotected DnaSequence
DnaSequence.factory()
Create a new sequenceprotected DnaSequence
DnaSequenceId.factory()
Create sequencesDnaSequencePe.getSeq1()
DnaSequencePe.getSeq2()
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Uses of DnaSequence in org.snpeff.binseq.comparator
Classes in org.snpeff.binseq.comparator with type parameters of type DnaSequenceModifier and TypeClassDescriptionclass
DnaSubsequenceComparator<T extends DnaSequence>
Compares two subsequences of DNA (DnaSequence)Methods in org.snpeff.binseq.comparator with parameters of type DnaSequenceModifier and TypeMethodDescriptionint
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 -
Uses of DnaSequence in org.snpeff.overlap
Methods in org.snpeff.overlap that return DnaSequenceModifier and TypeMethodDescriptionSequenceRotator.calcRor
(int rotate) SequenceRotator.rotate
(int rotate) Rotate leftMethods in org.snpeff.overlap with parameters of type DnaSequenceConstructors in org.snpeff.overlap with parameters of type DnaSequence