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} <=> {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(java.io.DataInputStream dataInStream)	Read a sequence from a data stream
BinarySequence	DnaNSequence.read(java.io.DataInputStream dataInStream)	Read data in binary format
BinarySequence	DnaSequence.read(java.io.DataInputStream dataInStream)	Read data in binary format
BinarySequence	DnaSequenceId.read(java.io.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.