sigalign_core/reference/sequence_storage/
mod.rs1use super::SequenceBuffer;
6pub trait SequenceStorage {
7 type Buffer: SequenceBuffer;
8
9 fn get_buffer(&self) -> Self::Buffer;
10 fn fill_buffer(&self, target_index: u32, buffer: &mut Self::Buffer);
11 fn num_targets(&self) -> u32;
12
13 fn get_concatenated_sequence_with_boundaries_of_targets(&self) -> (
14 Vec<u8>,
15 Vec<u32>,
16 ) {
17 let num_targets = self.num_targets();
18 let mut boundaries = Vec::with_capacity(num_targets as usize + 1);
19 boundaries.push(0);
20 let mut accumulated_length = 0;
21
22 let mut buffer = self.get_buffer();
23 let mut concatenated_sequence = Vec::new();
24 for target_index in 0..num_targets {
25 self.fill_buffer(target_index, &mut buffer);
26 let target_sequence = buffer.buffered_sequence();
27 accumulated_length += target_sequence.len() as u32;
28 boundaries.push(accumulated_length);
29 concatenated_sequence.extend_from_slice(target_sequence)
30 }
31
32 (
33 concatenated_sequence,
34 boundaries,
35 )
36 }
37}