Uses of Class
org.snpeff.binseq.BinarySequence
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Packages that use BinarySequence Package Description org.snpeff.binseq org.snpeff.binseq.comparator org.snpeff.binseq.indexer org.snpeff.fileIterator org.snpeff.overlap -
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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 IDclass
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 streamBinarySequence
DnaNSequence. read(java.io.DataInputStream dataInStream)
Read data in binary formatBinarySequence
DnaSequence. read(java.io.DataInputStream dataInStream)
Read data in binary formatBinarySequence
DnaSequenceId. read(java.io.DataInputStream dataInStream)
Read data in binary formatabstract BinarySequence
BinarySequence. reverseWc()
Reverse Watson-Cricks complementBinarySequence
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 notclass
OverlapRessult<T extends BinarySequence>
An object used to store overlap parametersclass
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
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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.
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