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Add scaling shifts for profile set all
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@Daniel-Liu-c0deb0t
Daniel-Liu-c0deb0t committed Jul 13, 2023
1 parent d812d58 commit 2bb6e44
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Showing 2 changed files with 55 additions and 158 deletions.
8 changes: 4 additions & 4 deletions src/ffi.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -98,11 +98,11 @@ pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u
/// Scores (in `scores`) should be stored in row-major order, where each row is a different position
/// and each column is a different byte.
#[no_mangle]
pub unsafe extern fn block_set_all_aaprofile(profile: *mut AAProfile, order: *const u8, order_len: usize, scores: *const i8, scores_len: usize) {
pub unsafe extern fn block_set_all_aaprofile(profile: *mut AAProfile, order: *const u8, order_len: usize, scores: *const i8, scores_len: usize, left_shift: usize, right_shift: usize) {
let profile = &mut *profile;
let order = std::slice::from_raw_parts(order, order_len);
let scores = std::slice::from_raw_parts(scores, scores_len);
profile.set_all(order, scores);
profile.set_all(order, scores, left_shift, right_shift);
}

/// Set the scores for all positions in reverse in the position specific scoring matrix.
Expand All @@ -113,11 +113,11 @@ pub unsafe extern fn block_set_all_aaprofile(profile: *mut AAProfile, order: *co
/// Scores (in `scores`) should be stored in row-major order, where each row is a different position
/// and each column is a different byte.
#[no_mangle]
pub unsafe extern fn block_set_all_rev_aaprofile(profile: *mut AAProfile, order: *const u8, order_len: usize, scores: *const i8, scores_len: usize) {
pub unsafe extern fn block_set_all_rev_aaprofile(profile: *mut AAProfile, order: *const u8, order_len: usize, scores: *const i8, scores_len: usize, left_shift: usize, right_shift: usize) {
let profile = &mut *profile;
let order = std::slice::from_raw_parts(order, order_len);
let scores = std::slice::from_raw_parts(scores, scores_len);
profile.set_all_rev(order, scores);
profile.set_all_rev(order, scores, left_shift, right_shift);
}

/// Set the gap open cost for a column.
Expand Down
205 changes: 51 additions & 154 deletions src/scores.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -367,15 +367,19 @@ pub trait Profile {
/// Use `order` to specify the order of bytes that is used in the `scores` matrix.
/// Scores (in `scores`) should be stored in row-major order, where each row is a different position
/// and each column is a different byte.
fn set_all(&mut self, order: &[u8], scores: &[i8]);
///
/// Use `left_shift` and `right_shift` to scale all the scores.
fn set_all(&mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize);
/// Set the scores for all positions in reverse in the position specific scoring matrix.
///
/// The profile should be first `clear`ed before it is reused with different lengths.
///
/// Use `order` to specify the order of bytes that is used in the `scores` matrix.
/// Scores (in `scores`) should be stored in row-major order, where each row is a different position
/// and each column is a different byte.
fn set_all_rev(&mut self, order: &[u8], scores: &[i8]);
///
/// Use `left_shift` and `right_shift` to scale all the scores.
fn set_all_rev(&mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize);

/// Set the gap open cost for a column.
///
Expand Down Expand Up @@ -518,160 +522,12 @@ impl Profile for AAProfile {
self.aa_pos[idx] = score as i16;
}

fn set_all(&mut self, order: &[u8], scores: &[i8]) {
#[repr(align(32))]
struct A([u8; 32]);
let mut o = A([Self::NULL - b'A'; 32]);
assert!(order.len() <= 32);

for (i, &b) in order.iter().enumerate() {
let b = b.to_ascii_uppercase();
assert!(b'A' <= b && b <= b'Z' + 1);
o.0[i] = b - b'A';
}
assert_eq!(scores.len() / order.len(), self.str_len);

let mut i = 1;
let mut score_idx = 0;

while i <= self.str_len {
let mut j = 0;

while j < order.len() {
// unroll 4 times for speed
if order.len() - j >= 4 {
unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;
} else {
unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;
}
}

i += 1;
}
fn set_all(&mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize) {
self.set_all_core::<false>(order, scores, left_shift, right_shift);
}

fn set_all_rev(&mut self, order: &[u8], scores: &[i8]) {
#[repr(align(32))]
struct A([u8; 32]);
let mut o = A([Self::NULL - b'A'; 32]);
assert!(order.len() <= 32);

for (i, &b) in order.iter().enumerate() {
let b = b.to_ascii_uppercase();
assert!(b'A' <= b && b <= b'Z' + 1);
o.0[i] = b - b'A';
}
assert_eq!(scores.len() / order.len(), self.str_len);

let mut i = self.str_len;
let mut score_idx = 0;

while i >= 1 {
let mut j = 0;

while j < order.len() {
// unroll 4 times for speed
if order.len() - j >= 4 {
unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;

unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;
} else {
unsafe {
let score = *scores.as_ptr().add(score_idx);
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;
}
}

i -= 1;
}
fn set_all_rev(&mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize) {
self.set_all_core::<true>(order, scores, left_shift, right_shift);
}

fn set_gap_open_C(&mut self, i: usize, gap: i8) {
Expand Down Expand Up @@ -809,3 +665,44 @@ impl Profile for AAProfile {
c - b'A'
}
}

impl AAProfile {
fn set_all_core<const REV: bool>(&mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize) {
#[repr(align(32))]
struct A([u8; 32]);
let mut o = A([Self::NULL - b'A'; 32]);
assert!(order.len() <= 32);

for (i, &b) in order.iter().enumerate() {
let b = b.to_ascii_uppercase();
assert!(b'A' <= b && b <= b'Z' + 1);
o.0[i] = b - b'A';
}
assert_eq!(scores.len() / order.len(), self.str_len);

let mut i = if REV { self.str_len } else { 1 };
let mut score_idx = 0;

while if REV { i >= 1 } else { i <= self.str_len } {
let mut j = 0;

while j < order.len() {
unsafe {
let score = ((*scores.as_ptr().add(score_idx)) << left_shift) >> right_shift;
let b = *o.0.as_ptr().add(j) as usize;
*self.pos_aa.as_mut_ptr().add(i * 32 + b) = score;
*self.aa_pos.as_mut_ptr().add(b * self.curr_len + i) = score as i16;
}

score_idx += 1;
j += 1;
}

if REV {
i -= 1;
} else {
i += 1;
}
}
}
}

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