/
minhash.rs
410 lines (335 loc) · 10.5 KB
/
minhash.rs
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use std::ffi::CStr;
use std::os::raw::c_char;
use std::slice;
use crate::ffi::utils::{ForeignObject, SourmashStr};
use crate::signature::SigsTrait;
use crate::sketch::minhash::{
aa_to_dayhoff, aa_to_hp, translate_codon, HashFunctions, KmerMinHash,
};
pub struct SourmashKmerMinHash;
impl ForeignObject for SourmashKmerMinHash {
type RustObject = KmerMinHash;
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_new(
n: u32,
k: u32,
prot: bool,
dayhoff: bool,
hp: bool,
seed: u64,
mx: u64,
track_abundance: bool,
) -> *mut SourmashKmerMinHash {
// TODO: at most one of (prot, dayhoff, hp) should be true
let hash_function = if dayhoff {
HashFunctions::murmur64_dayhoff
} else if hp {
HashFunctions::murmur64_hp
} else if prot {
HashFunctions::murmur64_protein
} else {
HashFunctions::murmur64_DNA
};
let mh = KmerMinHash::new(n, k, hash_function, seed, mx, track_abundance);
SourmashKmerMinHash::from_rust(mh)
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_free(ptr: *mut SourmashKmerMinHash) {
SourmashKmerMinHash::drop(ptr);
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_slice_free(ptr: *mut u64, insize: usize) {
// FIXME
if ptr.is_null() {
return;
}
Vec::from_raw_parts(ptr as *mut u64, insize, insize);
}
ffi_fn! {
unsafe fn kmerminhash_add_sequence(ptr: *mut SourmashKmerMinHash, sequence: *const c_char, force: bool) ->
Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: take buffer and len instead of c_char
let c_str = {
assert!(!sequence.is_null());
CStr::from_ptr(sequence)
};
mh.add_sequence(c_str.to_bytes(), force)
}
}
ffi_fn! {
unsafe fn kmerminhash_add_protein(ptr: *mut SourmashKmerMinHash, sequence: *const c_char) ->
Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: take buffer and len instead of c_char
let c_str = {
assert!(!sequence.is_null());
CStr::from_ptr(sequence)
};
mh.add_protein(c_str.to_bytes())
}
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_add_hash(ptr: *mut SourmashKmerMinHash, h: u64) {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
mh.add_hash(h);
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_add_word(ptr: *mut SourmashKmerMinHash, word: *const c_char) {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: take buffer and len instead of c_char
let c_str = {
assert!(!word.is_null());
CStr::from_ptr(word)
};
mh.add_word(c_str.to_bytes());
}
ffi_fn! {
unsafe fn sourmash_translate_codon(codon: *const c_char) -> Result<c_char> {
// FIXME: take buffer and len instead of c_char
let c_str = {
assert!(!codon.is_null());
CStr::from_ptr(codon)
};
Ok(translate_codon(c_str.to_bytes())? as c_char)
}
}
#[no_mangle]
pub unsafe extern "C" fn sourmash_aa_to_dayhoff(aa: c_char) -> c_char {
aa_to_dayhoff(aa as u8) as c_char
}
#[no_mangle]
pub unsafe extern "C" fn sourmash_aa_to_hp(aa: c_char) -> c_char {
aa_to_hp(aa as u8) as c_char
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_remove_hash(ptr: *mut SourmashKmerMinHash, h: u64) {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
mh.remove_hash(h);
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_remove_many(
ptr: *mut SourmashKmerMinHash,
hashes_ptr: *const u64,
insize: usize,
) {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: make a SourmashSlice_u64 type?
let hashes = {
assert!(!hashes_ptr.is_null());
slice::from_raw_parts(hashes_ptr as *mut u64, insize)
};
// FIXME: proper exception here
mh.remove_many(hashes).expect("Hash removal error");
}
ffi_fn! {
unsafe fn kmerminhash_get_mins(ptr: *const SourmashKmerMinHash, size: *mut usize) -> Result<*const u64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let output = mh.mins();
*size = output.len();
// FIXME: make a SourmashSlice_u64 type?
Ok(Box::into_raw(output.into_boxed_slice()) as *const u64)
}
}
ffi_fn! {
unsafe fn kmerminhash_md5sum(ptr: *const SourmashKmerMinHash) -> Result<SourmashStr> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let output = mh.md5sum();
Ok(output.into())
}
}
ffi_fn! {
unsafe fn kmerminhash_add_many(
ptr: *mut SourmashKmerMinHash,
hashes_ptr: *const u64,
insize: usize,
) -> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: make a SourmashSlice_u64 type?
let hashes = {
assert!(!hashes_ptr.is_null());
slice::from_raw_parts(hashes_ptr as *const u64, insize)
};
for hash in hashes {
mh.add_hash(*hash);
}
Ok(())
}
}
ffi_fn! {
unsafe fn kmerminhash_get_abunds(ptr: *mut SourmashKmerMinHash, size: *mut usize) -> Result<*const u64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
if let Some(abunds) = mh.abunds() {
*size = abunds.len();
Ok(Box::into_raw(abunds.into_boxed_slice()) as *const u64)
} else {
//throw error, can't get abund
unimplemented!()
}
}
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_get_mins_size(ptr: *const SourmashKmerMinHash) -> usize {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.size()
}
ffi_fn! {
unsafe fn kmerminhash_set_abundances(
ptr: *mut SourmashKmerMinHash,
hashes_ptr: *const u64,
abunds_ptr: *const u64,
insize: usize,
) -> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
// FIXME: make a SourmashSlice_u64 type?
let hashes = {
assert!(!hashes_ptr.is_null());
slice::from_raw_parts(hashes_ptr as *const u64, insize)
};
// FIXME: make a SourmashSlice_u64 type?
let abunds = {
assert!(!abunds_ptr.is_null());
slice::from_raw_parts(abunds_ptr as *const u64, insize)
};
let mut pairs: Vec<_> = hashes.iter().cloned().zip(abunds.iter().cloned()).collect();
pairs.sort();
// Reset the minhash
mh.clear();
mh.add_many_with_abund(&pairs)?;
Ok(())
}
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_is_protein(ptr: *const SourmashKmerMinHash) -> bool {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.is_protein()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_dayhoff(ptr: *const SourmashKmerMinHash) -> bool {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.dayhoff()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_hp(ptr: *const SourmashKmerMinHash) -> bool {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.hp()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_seed(ptr: *const SourmashKmerMinHash) -> u64 {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.seed()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_track_abundance(ptr: *const SourmashKmerMinHash) -> bool {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.track_abundance()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_disable_abundance(ptr: *mut SourmashKmerMinHash) {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
mh.disable_abundance();
}
ffi_fn! {
unsafe fn kmerminhash_enable_abundance(ptr: *mut SourmashKmerMinHash) -> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
mh.enable_abundance()?;
Ok(())
}
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_num(ptr: *const SourmashKmerMinHash) -> u32 {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.num()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_ksize(ptr: *const SourmashKmerMinHash) -> u32 {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.ksize() as u32
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_max_hash(ptr: *const SourmashKmerMinHash) -> u64 {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.max_hash()
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_hash_function(
ptr: *const SourmashKmerMinHash,
) -> HashFunctions {
let mh = SourmashKmerMinHash::as_rust(ptr);
mh.hash_function()
}
ffi_fn! {
unsafe fn kmerminhash_hash_function_set(ptr: *mut SourmashKmerMinHash, hash_function: HashFunctions) -> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
mh.set_hash_function(hash_function)
}
}
ffi_fn! {
unsafe fn kmerminhash_merge(ptr: *mut SourmashKmerMinHash, other: *const SourmashKmerMinHash) -> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.merge(other_mh)?;
Ok(())
}
}
#[no_mangle]
pub unsafe extern "C" fn kmerminhash_is_compatible(
ptr: *const SourmashKmerMinHash,
other: *const SourmashKmerMinHash,
) -> bool {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.check_compatible(other_mh).is_ok()
}
ffi_fn! {
unsafe fn kmerminhash_add_from(ptr: *mut SourmashKmerMinHash, other: *const SourmashKmerMinHash)
-> Result<()> {
let mh = SourmashKmerMinHash::as_rust_mut(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.add_from(other_mh)
}
}
ffi_fn! {
unsafe fn kmerminhash_count_common(ptr: *const SourmashKmerMinHash, other: *const SourmashKmerMinHash, downsample: bool)
-> Result<u64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.count_common(other_mh, downsample)
}
}
ffi_fn! {
unsafe fn kmerminhash_intersection(ptr: *const SourmashKmerMinHash, other: *const SourmashKmerMinHash)
-> Result<u64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
if let Ok((_, size)) = mh.intersection_size(other_mh) {
return Ok(size);
}
Ok(0)
}
}
ffi_fn! {
unsafe fn kmerminhash_jaccard(ptr: *const SourmashKmerMinHash, other: *const SourmashKmerMinHash)
-> Result<f64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.jaccard(other_mh)
}
}
ffi_fn! {
unsafe fn kmerminhash_similarity(ptr: *const SourmashKmerMinHash, other: *const SourmashKmerMinHash, ignore_abundance: bool, downsample: bool)
-> Result<f64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.similarity(other_mh, ignore_abundance, downsample)
}
}
ffi_fn! {
unsafe fn kmerminhash_angular_similarity(ptr: *const SourmashKmerMinHash, other: *const SourmashKmerMinHash)
-> Result<f64> {
let mh = SourmashKmerMinHash::as_rust(ptr);
let other_mh = SourmashKmerMinHash::as_rust(other);
mh.angular_similarity(other_mh)
}
}