Uses of Class
org.snpeff.binseq.DnaSequence
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Packages that use DnaSequence Package Description org.snpeff.binseq org.snpeff.binseq.comparator org.snpeff.interval org.snpeff.overlap -
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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 singletonprotected DnaSequence
DnaSequence. factory()
Create a new sequenceprotected DnaSequence
DnaSequenceId. factory()
Create sequencesDnaSequence
DnaSequencePe. getSeq1()
DnaSequence
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 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()
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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 leftMethods 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)
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