Trait SeqVec

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pub trait SeqVec:
    Default
    + Sync
    + SerializeInner
    + DeserializeInner
    + MemSize
    + MemDbg
    + Clone
    + 'static {
    type Seq<'s>: Seq<'s>;

Show 14 methods    // Required methods
    fn as_slice(&self) -> Self::Seq<'_>;
    fn len(&self) -> usize;
    fn is_empty(&self) -> bool;
    fn clear(&mut self);
    fn into_raw(self) -> Vec<u8> ⓘ;
    fn random(n: usize) -> Self;
    fn push_seq(&mut self, seq: Self::Seq<'_>) -> Range<usize>;
    fn push_ascii(&mut self, seq: &[u8]) -> Range<usize>;

    // Provided methods
    fn slice(&self, range: Range<usize>) -> Self::Seq<'_> { ... }
    fn read_kmer(&self, k: usize, pos: usize) -> u64 { ... }
    fn read_revcomp_kmer(&self, k: usize, pos: usize) -> u64 { ... }
    fn read_kmer_u128(&self, k: usize, pos: usize) -> u128 { ... }
    fn read_revcomp_kmer_u128(&self, k: usize, pos: usize) -> u128 { ... }
    fn from_ascii(seq: &[u8]) -> Self { ... }
}

Expand description

An owned sequence. Can be constructed from either ASCII input or the underlying non-owning Seq type.

Implemented for:

A Vec<u8> of ASCII characters, returning 8-bit values.
An AsciiSeqVec of DNA characters ACGT, interpreted as 2-bit values.
A PackedSeqVec of packed DNA characters (4 per byte), returning 2-bit values.

Required Associated Types§

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type Seq<'s>: Seq<'s>

Required Methods§

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fn as_slice(&self) -> Self::Seq<'_>

Get a non-owning slice to the underlying sequence.

Unfortunately, Deref into a Seq can not be supported.

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fn len(&self) -> usize

The length of the sequence in characters.

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fn is_empty(&self) -> bool

Returns true if the sequence is empty.

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fn clear(&mut self)

Empty the sequence.

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fn into_raw(self) -> Vec<u8> ⓘ

Convert into the underlying raw representation.

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fn random(n: usize) -> Self

Generate a random sequence with the given number of characters.

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fn push_seq(&mut self, seq: Self::Seq<'_>) -> Range<usize>

Append the given sequence to the underlying storage.

This may leave gaps (padding) between consecutively pushed sequences to avoid re-aligning the pushed data. Returns the range of indices corresponding to the pushed sequence. Use self.slice(range) to get the corresponding slice.

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fn push_ascii(&mut self, seq: &[u8]) -> Range<usize>

Append the given ASCII sequence to the underlying storage.

This may leave gaps (padding) between consecutively pushed sequences to avoid re-aligning the pushed data. Returns the range of indices corresponding to the pushed sequence. Use self.slice(range) to get the corresponding slice.