use crate::implementation::vec_sequence::VectorSubGenome;
use crate::interface::alphabet::{Alphabet, AlphabetCharacter, AlphabetError};
use crate::interface::sequence::GenomeSequence;
use crate::interface::sequence_store::{
HandleWithLength, HandleWithSubsequence, InverseMappingSequenceStore, SequenceStore,
};
use ref_cast::RefCast;
use std::marker::PhantomData;
use traitsequence::interface::Sequence;
#[derive(Default, Clone, Eq, PartialEq, Debug)]
pub struct VectorSequenceStore<AlphabetType: Alphabet> {
sequence: Vec<AlphabetType::CharacterType>,
}
#[derive(Default, Clone, Copy, Debug, Eq, PartialEq)]
pub struct VectorSequenceStoreHandle<AlphabetType: Alphabet> {
offset: usize,
len: usize,
phantom_data: PhantomData<AlphabetType>,
}
impl<AlphabetType: Alphabet> VectorSequenceStore<AlphabetType> {
pub fn new() -> Self {
Self {
sequence: Vec::new(),
}
}
}
impl<AlphabetType: Alphabet + 'static> SequenceStore<AlphabetType>
for VectorSequenceStore<AlphabetType>
{
type Handle = VectorSequenceStoreHandle<AlphabetType>;
type SequenceRef = VectorSubGenome<AlphabetType>;
fn add<
Sequence: GenomeSequence<AlphabetType, Subsequence> + ?Sized,
Subsequence: GenomeSequence<AlphabetType, Subsequence> + ?Sized,
>(
&mut self,
s: &Sequence,
) -> Self::Handle {
let offset = self.sequence.len();
let len = s.len();
self.sequence.extend(s.iter().cloned());
Self::Handle {
offset,
len,
phantom_data: Default::default(),
}
}
fn add_from_iter_u8<IteratorType: IntoIterator<Item = u8>>(
&mut self,
iter: IteratorType,
) -> Result<Self::Handle, AlphabetError> {
let offset = self.sequence.len();
let iter = iter.into_iter();
let (size, _) = iter.size_hint();
self.sequence.reserve(size);
for item in iter {
match AlphabetType::ascii_to_character(item) {
Ok(character) => self.sequence.push(character),
Err(error) => {
self.sequence
.resize(offset, AlphabetType::CharacterType::from_index(0).unwrap());
return Err(error);
}
}
}
let len = self.sequence.len() - offset;
Ok(Self::Handle {
offset,
len,
phantom_data: Default::default(),
})
}
fn get(&self, handle: &Self::Handle) -> &Self::SequenceRef {
VectorSubGenome::ref_cast(&self.sequence[handle.offset..handle.offset + handle.len])
}
}
impl<AlphabetType: Alphabet + 'static> InverseMappingSequenceStore<AlphabetType>
for VectorSequenceStore<AlphabetType>
{
fn map_sequence_ref_to_handle(&self, sequence_ref: &Self::SequenceRef) -> Self::Handle {
Self::Handle {
offset: (sequence_ref.slice.as_ptr() as usize) - (self.sequence.as_ptr() as usize),
len: sequence_ref.len(),
phantom_data: Default::default(),
}
}
}
impl<AlphabetType: Alphabet> HandleWithLength for VectorSequenceStoreHandle<AlphabetType> {
fn len(&self) -> usize {
self.len
}
}
impl<AlphabetType: Alphabet> HandleWithSubsequence<core::ops::Range<usize>>
for VectorSequenceStoreHandle<AlphabetType>
{
fn subsequence_handle(&self, range: core::ops::Range<usize>) -> Self {
let result = Self {
offset: self.offset + range.start,
len: range.end - range.start,
phantom_data: self.phantom_data,
};
debug_assert!(self.offset + self.len >= result.offset + result.len);
result
}
}