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clippy
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@luizirber
luizirber committed Jul 18, 2018
1 parent d475c8f commit b7d874c
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Showing 2 changed files with 108 additions and 116 deletions.
4 changes: 2 additions & 2 deletions src/ffi.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ pub extern "C" fn kmerminhash_track_abundance(ptr: *mut KmerMinHash) -> bool {
assert!(!ptr.is_null());
&mut *ptr
};
!mh.abunds.is_none()
mh.abunds.is_some()
}

#[no_mangle]
Expand Down Expand Up @@ -465,7 +465,7 @@ unsafe fn signature_eq(ptr: *mut Signature, other: *mut Signature) -> Result<boo
&mut *other
};

Ok(sig.eq(other_sig))
Ok(sig == other_sig)
}
}

Expand Down
220 changes: 106 additions & 114 deletions src/lib.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,18 +53,18 @@ pub struct NoHashHasher(u64);
impl Default for NoHashHasher {
#[inline]
fn default() -> NoHashHasher {
NoHashHasher(0x0000000000000000)
NoHashHasher(0x0)
}
}

impl Hasher for NoHashHasher {
#[inline]
fn write(&mut self, bytes: &[u8]) {
*self = NoHashHasher(
((bytes[0] as u64) << 24)
+ ((bytes[1] as u64) << 16)
+ ((bytes[2] as u64) << 8)
+ (bytes[3] as u64),
(u64::from(bytes[0]) << 24)
+ (u64::from(bytes[1]) << 16)
+ (u64::from(bytes[2]) << 8)
+ u64::from(bytes[3]),
);
}
fn finish(&self) -> u64 {
Expand Down Expand Up @@ -161,7 +161,7 @@ impl<'de> Deserialize<'de> for KmerMinHash {
let num = if tmpsig.max_hash != 0 { 0 } else { tmpsig.num };

Ok(KmerMinHash {
num: num,
num,
ksize: tmpsig.ksize,
seed: tmpsig.seed,
max_hash: tmpsig.max_hash,
Expand Down Expand Up @@ -233,7 +233,7 @@ impl KmerMinHash {
None => u64::max_value(),
};

if (self.max_hash != 0 && hash <= self.max_hash) || self.max_hash == 0 {
if hash <= self.max_hash || self.max_hash == 0 {
// empty? add it, if within range / no range specified.
if self.mins.is_empty() {
self.mins.push(hash);
Expand Down Expand Up @@ -271,11 +271,9 @@ impl KmerMinHash {
abunds.pop();
}
}
} else {
} else if let Some(ref mut abunds) = self.abunds {
// pos == hash: hash value already in mins, inc count
if let Some(ref mut abunds) = self.abunds {
abunds[pos] += 1;
}
abunds[pos] += 1;
}
}
}
Expand All @@ -302,12 +300,10 @@ impl KmerMinHash {
} else {
self.add_word(&rc);
}
} else {
if !force {
return Err(ErrorKind::InvalidDNA(
String::from_utf8(kmer.to_vec()).unwrap(),
).into());
}
} else if !force {
return Err(ErrorKind::InvalidDNA(
String::from_utf8(kmer.to_vec()).unwrap(),
).into());
}
}
} else {
Expand Down Expand Up @@ -368,7 +364,7 @@ impl KmerMinHash {

let mut self_value = self_iter.next();
let mut other_value = other_iter.next();
while !self_value.is_none() {
while self_value.is_some() {
let value = self_value.unwrap();
match other_value {
None => {
Expand Down Expand Up @@ -447,15 +443,15 @@ impl KmerMinHash {
Ok(())
}

pub fn add_many(&mut self, hashes: Vec<u64>) -> Result<()> {
for min in hashes.iter() {
pub fn add_many(&mut self, hashes: &[u64]) -> Result<()> {
for min in hashes {
self.add_hash(*min);
}
Ok(())
}

pub fn add_many_with_abund(&mut self, hashes: Vec<(u64, u64)>) -> Result<()> {
for item in hashes.iter() {
pub fn add_many_with_abund(&mut self, hashes: &[(u64, u64)]) -> Result<()> {
for item in hashes {
for _i in 0..item.1 {
self.add_hash(item.0);
}
Expand All @@ -481,7 +477,7 @@ impl KmerMinHash {
self.is_protein,
self.seed,
self.max_hash,
!self.abunds.is_none(),
self.abunds.is_some(),
);

combined_mh.merge(&self)?;
Expand Down Expand Up @@ -509,7 +505,7 @@ impl KmerMinHash {
self.is_protein,
self.seed,
self.max_hash,
!self.abunds.is_none(),
self.abunds.is_some(),
);

combined_mh.merge(&self)?;
Expand Down Expand Up @@ -585,20 +581,16 @@ impl Default for Signature {
}
}

impl Signature {
pub fn eq(&self, other: &Signature) -> bool {
let metadata = if self.class == other.class
impl PartialEq for Signature {
fn eq(&self, other: &Signature) -> bool {
let metadata = self.class == other.class
&& self.email == other.email
&& self.hash_function == other.hash_function
&& self.filename == other.filename
&& self.name == other.name
{
true
} else {
false
};
let mh = self.signatures.get(0).unwrap();
let other_mh = other.signatures.get(0).unwrap();
&& self.name == other.name;

let mh = &self.signatures[0];
let other_mh = &other.signatures[0];
metadata && (mh == other_mh)
}
}
Expand All @@ -621,85 +613,85 @@ lazy_static! {
static ref CODONTABLE: HashMap<&'static str, u8> = {
let mut m = HashMap::new();

m.insert("TTT", 'F' as u8);
m.insert("TTC", 'F' as u8);
m.insert("TTA", 'L' as u8);
m.insert("TTG", 'L' as u8);

m.insert("TCT", 'S' as u8);
m.insert("TCC", 'S' as u8);
m.insert("TCA", 'S' as u8);
m.insert("TCG", 'S' as u8);

m.insert("TAT", 'Y' as u8);
m.insert("TAC", 'Y' as u8);
m.insert("TAA", '*' as u8);
m.insert("TAG", '*' as u8);

m.insert("TGT", 'C' as u8);
m.insert("TGC", 'C' as u8);
m.insert("TGA", '*' as u8);
m.insert("TGG", 'W' as u8);

m.insert("CTT", 'L' as u8);
m.insert("CTC", 'L' as u8);
m.insert("CTA", 'L' as u8);
m.insert("CTG", 'L' as u8);

m.insert("CCT", 'P' as u8);
m.insert("CCC", 'P' as u8);
m.insert("CCA", 'P' as u8);
m.insert("CCG", 'P' as u8);

m.insert("CAT", 'H' as u8);
m.insert("CAC", 'H' as u8);
m.insert("CAA", 'Q' as u8);
m.insert("CAG", 'Q' as u8);

m.insert("CGT", 'R' as u8);
m.insert("CGC", 'R' as u8);
m.insert("CGA", 'R' as u8);
m.insert("CGG", 'R' as u8);

m.insert("ATT", 'I' as u8);
m.insert("ATC", 'I' as u8);
m.insert("ATA", 'I' as u8);
m.insert("ATG", 'M' as u8);

m.insert("ACT", 'T' as u8);
m.insert("ACC", 'T' as u8);
m.insert("ACA", 'T' as u8);
m.insert("ACG", 'T' as u8);

m.insert("AAT", 'N' as u8);
m.insert("AAC", 'N' as u8);
m.insert("AAA", 'K' as u8);
m.insert("AAG", 'K' as u8);

m.insert("AGT", 'S' as u8);
m.insert("AGC", 'S' as u8);
m.insert("AGA", 'R' as u8);
m.insert("AGG", 'R' as u8);

m.insert("GTT", 'V' as u8);
m.insert("GTC", 'V' as u8);
m.insert("GTA", 'V' as u8);
m.insert("GTG", 'V' as u8);

m.insert("GCT", 'A' as u8);
m.insert("GCC", 'A' as u8);
m.insert("GCA", 'A' as u8);
m.insert("GCG", 'A' as u8);

m.insert("GAT", 'D' as u8);
m.insert("GAC", 'D' as u8);
m.insert("GAA", 'E' as u8);
m.insert("GAG", 'E' as u8);

m.insert("GGT", 'G' as u8);
m.insert("GGC", 'G' as u8);
m.insert("GGA", 'G' as u8);
m.insert("GGG", 'G' as u8);
m.insert("TTT", b'F');
m.insert("TTC", b'F');
m.insert("TTA", b'L');
m.insert("TTG", b'L');

m.insert("TCT", b'S');
m.insert("TCC", b'S');
m.insert("TCA", b'S');
m.insert("TCG", b'S');

m.insert("TAT", b'Y');
m.insert("TAC", b'Y');
m.insert("TAA", b'*');
m.insert("TAG", b'*');

m.insert("TGT", b'C');
m.insert("TGC", b'C');
m.insert("TGA", b'*');
m.insert("TGG", b'W');

m.insert("CTT", b'L');
m.insert("CTC", b'L');
m.insert("CTA", b'L');
m.insert("CTG", b'L');

m.insert("CCT", b'P');
m.insert("CCC", b'P');
m.insert("CCA", b'P');
m.insert("CCG", b'P');

m.insert("CAT", b'H');
m.insert("CAC", b'H');
m.insert("CAA", b'Q');
m.insert("CAG", b'Q');

m.insert("CGT", b'R');
m.insert("CGC", b'R');
m.insert("CGA", b'R');
m.insert("CGG", b'R');

m.insert("ATT", b'I');
m.insert("ATC", b'I');
m.insert("ATA", b'I');
m.insert("ATG", b'M');

m.insert("ACT", b'T');
m.insert("ACC", b'T');
m.insert("ACA", b'T');
m.insert("ACG", b'T');

m.insert("AAT", b'N');
m.insert("AAC", b'N');
m.insert("AAA", b'K');
m.insert("AAG", b'K');

m.insert("AGT", b'S');
m.insert("AGC", b'S');
m.insert("AGA", b'R');
m.insert("AGG", b'R');

m.insert("GTT", b'V');
m.insert("GTC", b'V');
m.insert("GTA", b'V');
m.insert("GTG", b'V');

m.insert("GCT", b'A');
m.insert("GCC", b'A');
m.insert("GCA", b'A');
m.insert("GCG", b'A');

m.insert("GAT", b'D');
m.insert("GAC", b'D');
m.insert("GAA", b'E');
m.insert("GAG", b'E');

m.insert("GGT", b'G');
m.insert("GGC", b'G');
m.insert("GGA", b'G');
m.insert("GGG", b'G');

m
};
Expand Down

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