/
signature.rs
303 lines (252 loc) · 6.85 KB
/
signature.rs
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use std::convert::TryInto;
use std::ffi::CStr;
use std::io;
use std::os::raw::c_char;
use std::slice;
use niffler::get_input;
use serde_json;
use crate::ffi::utils::SourmashStr;
use crate::signature::Signature;
use crate::sketch::minhash::{HashFunctions, KmerMinHash};
use crate::sketch::Sketch;
// Signature methods
#[no_mangle]
pub unsafe extern "C" fn signature_new() -> *mut Signature {
Box::into_raw(Box::new(Signature::default())) as _
}
#[no_mangle]
pub unsafe extern "C" fn signature_free(ptr: *mut Signature) {
if ptr.is_null() {
return;
}
Box::from_raw(ptr);
}
ffi_fn! {
unsafe fn signature_set_name(ptr: *mut Signature, name: *const c_char) ->
Result<()> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let c_str = {
assert!(!name.is_null());
CStr::from_ptr(name)
};
if let Ok(name) = c_str.to_str() {
sig.name = Some(name.to_string())
}
Ok(())
}
}
ffi_fn! {
unsafe fn signature_set_filename(ptr: *mut Signature, name: *const c_char) ->
Result<()> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let c_str = {
assert!(!name.is_null());
CStr::from_ptr(name)
};
if let Ok(name) = c_str.to_str() {
sig.filename = Some(name.to_string())
}
Ok(())
}
}
ffi_fn! {
unsafe fn signature_push_mh(ptr: *mut Signature, other: *const KmerMinHash) ->
Result<()> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let mh = {
assert!(!other.is_null());
&*other
};
sig.signatures.push(Sketch::MinHash(mh.clone()));
Ok(())
}
}
ffi_fn! {
unsafe fn signature_set_mh(ptr: *mut Signature, other: *const KmerMinHash) ->
Result<()> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let mh = {
assert!(!other.is_null());
&*other
};
sig.signatures = vec![Sketch::MinHash(mh.clone())];
Ok(())
}
}
ffi_fn! {
unsafe fn signature_get_name(ptr: *mut Signature) -> Result<SourmashStr> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
if let Some(ref name) = sig.name {
Ok(SourmashStr::from_string(name.to_string()))
} else {
Ok(SourmashStr::from_string("".to_string()))
}
}
}
ffi_fn! {
unsafe fn signature_get_filename(ptr: *mut Signature) -> Result<SourmashStr> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
if let Some(ref name) = sig.filename {
Ok(SourmashStr::from_string(name.to_string()))
} else {
Ok(SourmashStr::from_string("".to_string()))
}
}
}
ffi_fn! {
unsafe fn signature_get_license(ptr: *mut Signature) -> Result<SourmashStr> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
Ok(SourmashStr::from_string(sig.license.to_string()))
}
}
ffi_fn! {
unsafe fn signature_first_mh(ptr: *mut Signature) -> Result<*mut KmerMinHash> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
if let Some(item) = sig.signatures.get(0) {
if let Sketch::MinHash(mh) = item {
Ok(Box::into_raw(Box::new(mh.clone())) as _)
} else {
unimplemented!()
}
} else {
// TODO: need to select the correct one
unimplemented!()
}
}
}
ffi_fn! {
unsafe fn signature_eq(ptr: *mut Signature, other: *mut Signature) -> Result<bool> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let other_sig = {
assert!(!other.is_null());
&mut *other
};
Ok(sig == other_sig)
}
}
ffi_fn! {
unsafe fn signature_save_json(ptr: *mut Signature) -> Result<SourmashStr> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let st = serde_json::to_string(sig)?;
Ok(SourmashStr::from_string(st))
}
}
ffi_fn! {
unsafe fn signature_get_mhs(ptr: *mut Signature, size: *mut usize) -> Result<*mut *mut KmerMinHash> {
let sig = {
assert!(!ptr.is_null());
&mut *ptr
};
let output = sig.signatures.clone();
let ptr_sigs: Vec<*mut Signature> = output.into_iter().map(|x| {
Box::into_raw(Box::new(x)) as *mut Signature
}).collect();
let b = ptr_sigs.into_boxed_slice();
*size = b.len();
Ok(Box::into_raw(b) as *mut *mut KmerMinHash)
}
}
ffi_fn! {
unsafe fn signatures_save_buffer(ptr: *mut *mut Signature, size: usize) -> Result<SourmashStr> {
let sigs = {
assert!(!ptr.is_null());
slice::from_raw_parts(ptr, size)
};
let rsigs: Vec<&Signature> = sigs.iter().map(|x| x.as_ref().unwrap()).collect();
let st = serde_json::to_string(&rsigs)?;
Ok(SourmashStr::from_string(st))
}
}
ffi_fn! {
unsafe fn signatures_load_path(ptr: *const c_char,
_ignore_md5sum: bool,
ksize: usize,
select_moltype: *const c_char,
size: *mut usize) -> Result<*mut *mut Signature> {
let buf = {
assert!(!ptr.is_null());
CStr::from_ptr(ptr)
};
let moltype: Option<HashFunctions> = if select_moltype.is_null() {
None
} else {
let mol = CStr::from_ptr(select_moltype).to_str()?;
Some(mol.try_into()?)
};
// TODO: implement ignore_md5sum
let k = match ksize {
0 => None,
x => Some(x)
};
let (mut input, _) = get_input(buf.to_str()?)?;
let filtered_sigs = Signature::load_signatures(&mut input, k, moltype, None)?;
let ptr_sigs: Vec<*mut Signature> = filtered_sigs.into_iter().map(|x| {
Box::into_raw(Box::new(x)) as *mut Signature
}).collect();
let b = ptr_sigs.into_boxed_slice();
*size = b.len();
Ok(Box::into_raw(b) as *mut *mut Signature)
}
}
ffi_fn! {
unsafe fn signatures_load_buffer(ptr: *const c_char,
insize: usize,
_ignore_md5sum: bool,
ksize: usize,
select_moltype: *const c_char,
size: *mut usize) -> Result<*mut *mut Signature> {
let buf = {
assert!(!ptr.is_null());
slice::from_raw_parts(ptr as *mut u8, insize)
};
let moltype: Option<HashFunctions> = if select_moltype.is_null() {
None
} else {
let mol = CStr::from_ptr(select_moltype).to_str()?;
Some(mol.try_into()?)
};
let k = match ksize {
0 => None,
x => Some(x)
};
// TODO: implement ignore_md5sum
let mut reader = io::BufReader::new(buf);
let filtered_sigs = Signature::load_signatures(&mut reader, k, moltype, None)?;
let ptr_sigs: Vec<*mut Signature> = filtered_sigs.into_iter().map(|x| {
Box::into_raw(Box::new(x)) as *mut Signature
}).collect();
let b = ptr_sigs.into_boxed_slice();
*size = b.len();
Ok(Box::into_raw(b) as *mut *mut Signature)
}
}