Trait GenomeSequence 

pub trait GenomeSequence<AlphabetType: Alphabet, GenomeSubsequence: GenomeSequence<AlphabetType, GenomeSubsequence> + ?Sized>: Sequence<AlphabetType::CharacterType, GenomeSubsequence> {
    // Provided methods
    fn is_valid(&self) -> bool { ... }
    fn clone_as_vec(&self) -> Vec<u8>  { ... }
    fn as_genome_subsequence(&self) -> &GenomeSubsequence { ... }
    fn as_string(&self) -> String { ... }
    fn reverse_complement_iter(
        &self,
    ) -> ReverseComplementIterator<Self::Iterator<'_>, AlphabetType> { ... }
    fn cloned_k_mer_iter<const K: usize, KmerType: OwnedKmer<K, AlphabetType, GenomeSubsequence>>(
        &self,
    ) -> OwnedKmerIterator<'_, Self, KmerType> { ... }
    fn convert_with_reverse_complement<ReverseComplementSequence: OwnedGenomeSequence<AlphabetType, ReverseComplementSubsequence>, ReverseComplementSubsequence: GenomeSequence<AlphabetType, ReverseComplementSubsequence> + ?Sized>(
        &self,
    ) -> ReverseComplementSequence { ... }
    fn convert<ResultSequence: OwnedGenomeSequence<AlphabetType, ResultSubsequence>, ResultSubsequence: GenomeSequence<AlphabetType, ResultSubsequence> + ?Sized>(
        &self,
    ) -> ResultSequence { ... }
    fn is_canonical(&self) -> bool { ... }
    fn is_self_complemental(&self) -> bool { ... }
}

A genome sequence.

Provided Methods

fn is_valid(&self) -> bool

Returns true if this genome is valid, i.e. it contains no invalid characters.

fn clone_as_vec(&self) -> Vec<u8>

Copies this genome string into a Vec.

fn as_genome_subsequence(&self) -> &GenomeSubsequence

Get a reference to this genome as its subsequence type.

fn as_string(&self) -> String

Returns the genome as nucleotide string.

fn reverse_complement_iter( &self, ) -> ReverseComplementIterator<Self::Iterator<'_>, AlphabetType>

Returns an iterator over the reverse complement of this genome. Panics if the iterator his an invalid character (see not valid).

fn cloned_k_mer_iter<const K: usize, KmerType: OwnedKmer<K, AlphabetType, GenomeSubsequence>>( &self, ) -> OwnedKmerIterator<'_, Self, KmerType>

Returns an iterator over the k-mers of this genome. The k-mers are cloned from this genome.

fn convert_with_reverse_complement<ReverseComplementSequence: OwnedGenomeSequence<AlphabetType, ReverseComplementSubsequence>, ReverseComplementSubsequence: GenomeSequence<AlphabetType, ReverseComplementSubsequence> + ?Sized>( &self, ) -> ReverseComplementSequence

Returns an owned copy of the reverse complement of this genome. Panics if this genome is not valid.

fn convert<ResultSequence: OwnedGenomeSequence<AlphabetType, ResultSubsequence>, ResultSubsequence: GenomeSequence<AlphabetType, ResultSubsequence> + ?Sized>( &self, ) -> ResultSequence

Returns an owned copy of this genome.

fn is_canonical(&self) -> bool

Returns true if the genome is canonical. A canonical genome is lexicographically smaller or equal to its reverse complement.

fn is_self_complemental(&self) -> bool

Returns true if the genome is self-complemental. A self-complemental genome is equivalent to its reverse complement.

Dyn Compatibility

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety", so this trait is not object safe.

Implementors

impl<AlphabetType: Alphabet> GenomeSequence<AlphabetType, SliceSubGenome<AlphabetType>> for SliceSubGenome<AlphabetType>

impl<AlphabetType: Alphabet> GenomeSequence<AlphabetType, SliceSubGenome<AlphabetType>> for VectorGenome<AlphabetType>

impl<AlphabetType: Alphabet, BitStoreType: BitStore> GenomeSequence<AlphabetType, BitVectorSubGenome<AlphabetType, BitStoreType>> for BitVectorGenome<AlphabetType, BitStoreType>

impl<AlphabetType: Alphabet, BitStoreType: BitStore> GenomeSequence<AlphabetType, BitVectorSubGenome<AlphabetType, BitStoreType>> for BitVectorSubGenome<AlphabetType, BitStoreType>

impl<const K: usize, AlphabetType: Alphabet> GenomeSequence<AlphabetType, SliceSubGenome<AlphabetType>> for ArrayKmer<K, AlphabetType>

impl<const K: usize, AlphabetType: Alphabet, BitArrayType: BitViewSized + BitStore + BitView<Store = BitArrayType>> GenomeSequence<AlphabetType, BitVectorSubGenome<AlphabetType, BitArrayType>> for BitArrayKmer<K, AlphabetType, BitArrayType>