# Uses of Class
org.snpeff.binseq.BinarySequence

Packages that use BinarySequence
Package
Description
org.snpeff.binseq
org.snpeff.binseq.comparator
org.snpeff.binseq.indexer
org.snpeff.fileIterator
org.snpeff.overlap

## Uses of BinarySequence in org.snpeff.binseq

Subclasses of BinarySequence in org.snpeff.binseq
Modifier and Type
Class
Description
`class`
`DnaAndQualitySequence`
Binary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..
`class`
`DnaAndQualitySequenceWithId`
DnaAndQualitySequence with an ID
`class`
`DnaNSequence`
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
`class`
`DnaSequence`
Binary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} invalid input: '<'=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)
`class`
`DnaSequenceId`
Binary packed DNA sequence with an ID (long)
`class`
`DnaSequencePe`
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
Methods in org.snpeff.binseq that return BinarySequence
Modifier and Type
Method
Description
`BinarySequence`
BinarySequence.`clone()`
`BinarySequence`
BinarySequence.`overlap(BinarySequence sequence, int start)`
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
`BinarySequence`
DnaSequence.`overlap(BinarySequence sequence, int start)`
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
`abstract BinarySequence`
BinarySequence.`read(DataInputStream dataInStream)`
Read a sequence from a data stream
`BinarySequence`
DnaNSequence.`read(DataInputStream dataInStream)`
Read data in binary format
`BinarySequence`
DnaSequence.`read(DataInputStream dataInStream)`
Read data in binary format
`BinarySequence`
DnaSequenceId.`read(DataInputStream dataInStream)`
Read data in binary format
`abstract BinarySequence`
BinarySequence.`reverseWc()`
Reverse Watson-Cricks complement
`BinarySequence`
DnaNSequence.`reverseWc()`
`BinarySequence`
DnaSequence.`reverseWc()`
`BinarySequence`
DnaSequencePe.`reverseWc()`
Methods in org.snpeff.binseq with parameters of type BinarySequence
Modifier and Type
Method
Description
`int`
DnaAndQualitySequence.`compareTo(BinarySequence o)`
`int`
DnaSequence.`compareTo(BinarySequence o)`
`int`
DnaSequencePe.`compareTo(BinarySequence o)`
`BinarySequence`
BinarySequence.`overlap(BinarySequence sequence, int start)`
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
`DnaAndQualitySequence`
DnaAndQualitySequence.`overlap(BinarySequence sequence, int start)`
Creates a new sequence by overlapping 'this' and 'sequence' E.g.
`BinarySequence`
DnaSequence.`overlap(BinarySequence sequence, int start)`
Creates a new sequence by overlapping 'this' and 'sequence' E.g.

## Uses of BinarySequence in org.snpeff.binseq.comparator

Classes in org.snpeff.binseq.comparator with type parameters of type BinarySequence
Modifier and Type
Class
Description
`class`
`SubsequenceComparator<T extends BinarySequence>`
Compare two subsequences (actually it compares two sequences from different starting points)

## Uses of BinarySequence in org.snpeff.binseq.indexer

Classes in org.snpeff.binseq.indexer with type parameters of type BinarySequence
Modifier and Type
Interface
Description
`interface`
`OverlapFilter<T extends BinarySequence>`
Indicate whether an overlap between two sequences should be considered or not
`class`
`OverlapRessult<T extends BinarySequence>`
An object used to store overlap parameters
`class`
`SequenceIndexer<T extends BinarySequence>`
A collection of sequences that are indexed using some algorithm Note: The ID is just the position in the array.
`class`
`SuffixIndexerNmer<T extends BinarySequence>`
Index all suffixes of all the sequences (it indexes using Nmers).
Fields in org.snpeff.binseq.indexer declared as BinarySequence
Modifier and Type
Field
Description
`T`
OverlapRessult.`bestSequence`

## Uses of BinarySequence in org.snpeff.fileIterator

Classes in org.snpeff.fileIterator with type parameters of type BinarySequence
Modifier and Type
Class
Description
`class`
`BinSeqFileIterator<T extends BinarySequence>`
Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.

## Uses of BinarySequence in org.snpeff.overlap

Classes in org.snpeff.overlap with type parameters of type BinarySequence
Modifier and Type
Class
Description
`class`
`Overlap<S extends BinarySequence>`
Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.