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use std::os::raw::c_int;
use crate::bitmap::set;
use crate::sequence::rcom_seq;
use crate::types::{Gene, Mask, Node, MASK_SIZE, MAX_GENES, MAX_MASKS, MAX_SEQ, STT_NOD};
/// Internal scratch buffers for the prediction pipeline.
pub(crate) struct SequenceBuffer {
pub seq: Vec<u8>,
pub rseq: Vec<u8>,
pub useq: Vec<u8>,
pub nodes: Vec<Node>,
pub genes: Vec<Gene>,
pub masks: Vec<Mask>,
pub nmask: c_int,
}
impl SequenceBuffer {
pub fn new() -> Self {
SequenceBuffer {
seq: vec![0u8; MAX_SEQ / 4],
rseq: vec![0u8; MAX_SEQ / 4],
useq: vec![0u8; MAX_SEQ / 8],
nodes: vec![unsafe { std::mem::zeroed() }; STT_NOD],
genes: vec![unsafe { std::mem::zeroed() }; MAX_GENES],
masks: vec![unsafe { std::mem::zeroed() }; MAX_MASKS],
nmask: 0,
}
}
/// Clear sequence buffers for a new sequence.
fn clear_seq(&mut self, prev_len: usize) {
let seq_bytes = (prev_len / 4 + 1).min(self.seq.len());
let useq_bytes = (prev_len / 8 + 1).min(self.useq.len());
self.seq[..seq_bytes].fill(0);
self.rseq[..seq_bytes].fill(0);
self.useq[..useq_bytes].fill(0);
self.nmask = 0;
}
/// Encode a single DNA sequence into the internal 2-bit bitmap format.
/// Returns (sequence_length, gc_content).
pub unsafe fn encode(&mut self, dna: &[u8], do_mask: bool) -> (c_int, f64) {
self.clear_seq(self.seq.len() * 4);
let mut bctr: c_int = 0;
let mut len: c_int = 0;
let mut gc_count: c_int = 0;
let mut mask_beg: c_int = -1;
for &base in dna {
if base < b'A' || base > b'z' {
continue;
}
// Handle mask tracking
if do_mask && mask_beg != -1 && base != b'N' && base != b'n' {
if len - mask_beg >= MASK_SIZE as c_int {
if (self.nmask as usize) < MAX_MASKS {
self.masks[self.nmask as usize].begin = mask_beg;
self.masks[self.nmask as usize].end = len - 1;
self.nmask += 1;
}
}
mask_beg = -1;
}
if do_mask && mask_beg == -1 && (base == b'N' || base == b'n') {
mask_beg = len;
}
match base {
b'g' | b'G' => {
set(self.seq.as_mut_ptr(), bctr);
gc_count += 1;
}
b't' | b'T' => {
set(self.seq.as_mut_ptr(), bctr);
set(self.seq.as_mut_ptr(), bctr + 1);
}
b'c' | b'C' => {
set(self.seq.as_mut_ptr(), bctr + 1);
gc_count += 1;
}
b'a' | b'A' => { /* bits 00, nothing to set */ }
_ => {
// Unknown base (N, etc.)
set(self.seq.as_mut_ptr(), bctr + 1);
set(self.useq.as_mut_ptr(), len);
}
}
bctr += 2;
len += 1;
}
if len > 0 {
rcom_seq(
self.seq.as_mut_ptr(),
self.rseq.as_mut_ptr(),
self.useq.as_mut_ptr(),
len,
);
}
let gc = if len > 0 {
gc_count as f64 / len as f64
} else {
0.0
};
(len, gc)
}
/// Encode multiple sequences concatenated with TTAATTAATTAA spacers.
/// Used for training (mirrors read_seq_training behavior).
/// Returns (total_length, gc_content).
pub unsafe fn encode_training(&mut self, sequences: &[&[u8]], do_mask: bool) -> (c_int, f64) {
self.clear_seq(self.seq.len() * 4);
let mut bctr: c_int = 0;
let mut len: c_int = 0;
let mut gc_count: c_int = 0;
let mut mask_beg: c_int = -1;
let mut seq_count = 0;
for &seq_data in sequences {
// Insert TTAATTAATTAA spacer between sequences
if seq_count > 0 {
// 12 bases: T T A A T T A A T T A A
for i in 0..12 {
if i % 4 == 0 || i % 4 == 1 {
set(self.seq.as_mut_ptr(), bctr);
set(self.seq.as_mut_ptr(), bctr + 1);
}
bctr += 2;
len += 1;
}
}
seq_count += 1;
for &base in seq_data {
if base < b'A' || base > b'z' {
continue;
}
if do_mask && mask_beg != -1 && base != b'N' && base != b'n' {
if len - mask_beg >= MASK_SIZE as c_int {
if (self.nmask as usize) < MAX_MASKS {
self.masks[self.nmask as usize].begin = mask_beg;
self.masks[self.nmask as usize].end = len - 1;
self.nmask += 1;
}
}
mask_beg = -1;
}
if do_mask && mask_beg == -1 && (base == b'N' || base == b'n') {
mask_beg = len;
}
match base {
b'g' | b'G' => {
set(self.seq.as_mut_ptr(), bctr);
gc_count += 1;
}
b't' | b'T' => {
set(self.seq.as_mut_ptr(), bctr);
set(self.seq.as_mut_ptr(), bctr + 1);
}
b'c' | b'C' => {
set(self.seq.as_mut_ptr(), bctr + 1);
gc_count += 1;
}
b'a' | b'A' => {}
_ => {
set(self.seq.as_mut_ptr(), bctr + 1);
set(self.useq.as_mut_ptr(), len);
}
}
bctr += 2;
len += 1;
if (len as usize) + 10000 >= MAX_SEQ {
break;
}
}
}
// Add trailing spacer if multiple sequences
if seq_count > 1 {
for i in 0..12 {
if i % 4 == 0 || i % 4 == 1 {
set(self.seq.as_mut_ptr(), bctr);
set(self.seq.as_mut_ptr(), bctr + 1);
}
bctr += 2;
len += 1;
}
}
if len > 0 {
rcom_seq(
self.seq.as_mut_ptr(),
self.rseq.as_mut_ptr(),
self.useq.as_mut_ptr(),
len,
);
}
let gc = if len > 0 {
gc_count as f64 / len as f64
} else {
0.0
};
(len, gc)
}
/// Ensure node buffer is large enough for the given sequence length.
pub fn ensure_node_capacity(&mut self, slen: c_int) {
let needed = (slen as usize) / 8;
if needed > self.nodes.len() {
self.nodes.resize(needed, unsafe { std::mem::zeroed() });
}
}
/// Clear node buffer.
pub fn clear_nodes(&mut self, nn: c_int) {
for i in 0..(nn as usize).min(self.nodes.len()) {
self.nodes[i] = unsafe { std::mem::zeroed() };
}
}
}