compact_genome/implementation/
handle_sequence_store.rs

1//! An "anti" sequence store that stores the sequences in the handles.
2//!
3//! This is useful to use methods that require a sequence store when only plain sequences are available.
4
5use std::marker::PhantomData;
6
7use crate::interface::{
8    alphabet::{Alphabet, AlphabetError},
9    sequence::{GenomeSequence, OwnedGenomeSequence},
10    sequence_store::SequenceStore,
11};
12
13/// A handle-based sequence store.
14///
15/// The sequence store stores nothing, all data is in the handles.
16#[derive(Default, Clone, Eq, PartialEq, Debug)]
17pub struct HandleSequenceStore<AlphabetType, SequenceType, SubsequenceType: ?Sized> {
18    phantom_data: PhantomData<(AlphabetType, SequenceType, SubsequenceType)>,
19}
20
21impl<AlphabetType, SequenceType, SubsequenceType: ?Sized>
22    HandleSequenceStore<AlphabetType, SequenceType, SubsequenceType>
23{
24    /// Creates a new instance.
25    pub fn new() -> Self {
26        Self {
27            phantom_data: Default::default(),
28        }
29    }
30}
31
32impl<
33        AlphabetType: Alphabet,
34        SequenceType: OwnedGenomeSequence<AlphabetType, SubsequenceType>,
35        SubsequenceType: GenomeSequence<AlphabetType, SubsequenceType> + ?Sized,
36    > SequenceStore<AlphabetType>
37    for HandleSequenceStore<AlphabetType, SequenceType, SubsequenceType>
38{
39    type Handle = SequenceType;
40    type SequenceRef = SubsequenceType;
41
42    fn add<
43        Sequence: GenomeSequence<AlphabetType, Subsequence> + ?Sized,
44        Subsequence: GenomeSequence<AlphabetType, Subsequence> + ?Sized,
45    >(
46        &mut self,
47        s: &Sequence,
48    ) -> Self::Handle {
49        Self::Handle::from_iter(s.iter().cloned())
50    }
51
52    fn add_from_iter(
53        &mut self,
54        iter: impl IntoIterator<Item = <AlphabetType as Alphabet>::CharacterType>,
55    ) -> Self::Handle {
56        Self::Handle::from_iter(iter)
57    }
58
59    fn add_from_iter_u8<IteratorType: IntoIterator<Item = u8>>(
60        &mut self,
61        iter: IteratorType,
62    ) -> Result<Self::Handle, AlphabetError> {
63        Self::Handle::from_iter_u8(iter)
64    }
65
66    fn get<'this: 'result, 'handle: 'result, 'result>(
67        &'this self,
68        handle: &'handle Self::Handle,
69    ) -> &'result Self::SequenceRef {
70        handle.as_genome_subsequence()
71    }
72}
compact_genome/implementation/handle_sequence_store.rs

compact_genome/implementation/
handle_sequence_store.rs
