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douweschultedouweschulte
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Fix clippy lints and remove possible crash in align
1 parent 10136ec commit 8524b24

5 files changed

Lines changed: 142 additions & 124 deletions

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‎mzalign/src/align_matrix.rs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -84,8 +84,8 @@ impl Matrix {
8484
}
8585
high = (
8686
0,
87-
high.1 - value.step_a as usize,
88-
high.2 - value.step_b as usize,
87+
high.1.saturating_sub(value.step_a as usize),
88+
high.2.saturating_sub(value.step_b as usize),
8989
);
9090
path.push(value);
9191
}

‎mzannotate/src/fragment/mzpaf/read.rs‎

Lines changed: 135 additions & 117 deletions
Original file line numberDiff line numberDiff line change
@@ -137,17 +137,20 @@ fn parse_annotation<'a>(
137137
let (left_range, charge) = parse_charge(base_context, line, left_range)?;
138138
let (left_range, deviation) = parse_deviation(base_context, line, left_range)?;
139139
let (left_range, confidence) = parse_confidence(base_context, line, left_range)?;
140-
Ok((left_range, PeakAnnotation {
141-
auxiliary,
142-
analyte_number,
143-
ion,
144-
neutral_losses,
145-
isotopes,
146-
charge: adduct_type
147-
.unwrap_or_else(|| MolecularCharge::proton(Charge::new::<e>(charge.value))),
148-
deviation,
149-
confidence,
150-
}))
140+
Ok((
141+
left_range,
142+
PeakAnnotation {
143+
auxiliary,
144+
analyte_number,
145+
ion,
146+
neutral_losses,
147+
isotopes,
148+
charge: adduct_type
149+
.unwrap_or_else(|| MolecularCharge::proton(Charge::new::<e>(charge.value))),
150+
deviation,
151+
confidence,
152+
},
153+
))
151154
}
152155

153156
/// An mzPAF single peak annotation.
@@ -238,104 +241,119 @@ impl PeakAnnotation {
238241
} else {
239242
(0, AminoAcid::Unknown, AminoAcid::Unknown)
240243
};
241-
(None, match series {
242-
b'a' => FragmentType::a(
243-
PeptidePosition {
244-
sequence_index: SequencePosition::Index(ordinal - 1, sequence_length),
245-
series_number: ordinal,
246-
sequence_length,
247-
},
248-
variant,
249-
),
250-
b'b' => FragmentType::b(
251-
PeptidePosition {
252-
sequence_index: SequencePosition::Index(ordinal - 1, sequence_length),
253-
series_number: ordinal,
254-
sequence_length,
255-
},
256-
variant,
257-
),
258-
b'c' => FragmentType::c(
259-
PeptidePosition {
260-
sequence_index: SequencePosition::Index(ordinal - 1, sequence_length),
261-
series_number: ordinal,
262-
sequence_length,
263-
},
264-
variant,
265-
),
266-
b'd' => FragmentType::d(
267-
PeptidePosition {
268-
sequence_index: SequencePosition::Index(ordinal - 1, sequence_length),
269-
series_number: ordinal,
270-
sequence_length,
271-
},
272-
n_aa,
273-
0,
274-
variant,
275-
sub,
276-
),
277-
b'v' => FragmentType::v(
278-
PeptidePosition {
279-
sequence_index: SequencePosition::Index(
280-
sequence_length.saturating_sub(ordinal),
244+
(
245+
None,
246+
match series {
247+
b'a' => FragmentType::a(
248+
PeptidePosition {
249+
sequence_index: SequencePosition::Index(
250+
ordinal - 1,
251+
sequence_length,
252+
),
253+
series_number: ordinal,
281254
sequence_length,
282-
),
283-
series_number: ordinal,
284-
sequence_length,
285-
},
286-
c_aa,
287-
0,
288-
variant,
289-
),
290-
b'w' => FragmentType::w(
291-
PeptidePosition {
292-
sequence_index: SequencePosition::Index(
293-
sequence_length.saturating_sub(ordinal),
255+
},
256+
variant,
257+
),
258+
b'b' => FragmentType::b(
259+
PeptidePosition {
260+
sequence_index: SequencePosition::Index(
261+
ordinal - 1,
262+
sequence_length,
263+
),
264+
series_number: ordinal,
294265
sequence_length,
295-
),
296-
series_number: ordinal,
297-
sequence_length,
298-
},
299-
c_aa,
300-
0,
301-
variant,
302-
sub,
303-
),
304-
b'x' => FragmentType::x(
305-
PeptidePosition {
306-
sequence_index: SequencePosition::Index(
307-
sequence_length.saturating_sub(ordinal),
266+
},
267+
variant,
268+
),
269+
b'c' => FragmentType::c(
270+
PeptidePosition {
271+
sequence_index: SequencePosition::Index(
272+
ordinal - 1,
273+
sequence_length,
274+
),
275+
series_number: ordinal,
308276
sequence_length,
309-
),
310-
series_number: ordinal,
311-
sequence_length,
312-
},
313-
variant,
314-
),
315-
b'y' => FragmentType::y(
316-
PeptidePosition {
317-
sequence_index: SequencePosition::Index(
318-
sequence_length.saturating_sub(ordinal),
277+
},
278+
variant,
279+
),
280+
b'd' => FragmentType::d(
281+
PeptidePosition {
282+
sequence_index: SequencePosition::Index(
283+
ordinal - 1,
284+
sequence_length,
285+
),
286+
series_number: ordinal,
319287
sequence_length,
320-
),
321-
series_number: ordinal,
322-
sequence_length,
323-
},
324-
variant,
325-
),
326-
b'z' => FragmentType::z(
327-
PeptidePosition {
328-
sequence_index: SequencePosition::Index(
329-
sequence_length.saturating_sub(ordinal),
288+
},
289+
n_aa,
290+
0,
291+
variant,
292+
sub,
293+
),
294+
b'v' => FragmentType::v(
295+
PeptidePosition {
296+
sequence_index: SequencePosition::Index(
297+
sequence_length.saturating_sub(ordinal),
298+
sequence_length,
299+
),
300+
series_number: ordinal,
330301
sequence_length,
331-
),
332-
series_number: ordinal,
333-
sequence_length,
334-
},
335-
variant,
336-
),
337-
_ => unreachable!(),
338-
})
302+
},
303+
c_aa,
304+
0,
305+
variant,
306+
),
307+
b'w' => FragmentType::w(
308+
PeptidePosition {
309+
sequence_index: SequencePosition::Index(
310+
sequence_length.saturating_sub(ordinal),
311+
sequence_length,
312+
),
313+
series_number: ordinal,
314+
sequence_length,
315+
},
316+
c_aa,
317+
0,
318+
variant,
319+
sub,
320+
),
321+
b'x' => FragmentType::x(
322+
PeptidePosition {
323+
sequence_index: SequencePosition::Index(
324+
sequence_length.saturating_sub(ordinal),
325+
sequence_length,
326+
),
327+
series_number: ordinal,
328+
sequence_length,
329+
},
330+
variant,
331+
),
332+
b'y' => FragmentType::y(
333+
PeptidePosition {
334+
sequence_index: SequencePosition::Index(
335+
sequence_length.saturating_sub(ordinal),
336+
sequence_length,
337+
),
338+
series_number: ordinal,
339+
sequence_length,
340+
},
341+
variant,
342+
),
343+
b'z' => FragmentType::z(
344+
PeptidePosition {
345+
sequence_index: SequencePosition::Index(
346+
sequence_length.saturating_sub(ordinal),
347+
sequence_length,
348+
),
349+
series_number: ordinal,
350+
sequence_length,
351+
},
352+
variant,
353+
),
354+
_ => unreachable!(),
355+
},
356+
)
339357
}
340358
IonType::Immonium(aa, m) => (
341359
aa.calculate_masses::<OutputMolecularFormula>().first().map(|f| {
@@ -902,7 +920,7 @@ fn parse_ion<'a>(
902920
BasicKind::Error,
903921
"Invalid mzPAF SMILES",
904922
"The SMILES string is charged",
905-
base_context.clone().add_highlight((0, smiles_range.clone())),
923+
base_context.clone().add_highlight((0, smiles_range)),
906924
));
907925
}
908926
let composition = structure.composition().ok_or_else(|| {
@@ -1494,24 +1512,24 @@ static MZPAF_NAMED_MOLECULES: LazyLock<Vec<(&str, MolecularFormula)>> = LazyLock
14941512
fn neutral_loss() {
14951513
assert_eq!(
14961514
parse_neutral_loss(&Context::default(), "-H2O", 0..4),
1497-
Ok((4..4, vec![NeutralLoss::Loss(
1498-
1,
1499-
molecular_formula!(H 2 O 1)
1500-
)]))
1515+
Ok((
1516+
4..4,
1517+
vec![NeutralLoss::Loss(1, molecular_formula!(H 2 O 1))]
1518+
))
15011519
);
15021520
assert_eq!(
15031521
parse_neutral_loss(&Context::default(), "+H2O", 0..4),
1504-
Ok((4..4, vec![NeutralLoss::Gain(
1505-
1,
1506-
molecular_formula!(H 2 O 1)
1507-
)]))
1522+
Ok((
1523+
4..4,
1524+
vec![NeutralLoss::Gain(1, molecular_formula!(H 2 O 1))]
1525+
))
15081526
);
15091527
assert_eq!(
15101528
parse_neutral_loss(&Context::default(), "+NH3", 0..4),
1511-
Ok((4..4, vec![NeutralLoss::Gain(
1512-
1,
1513-
molecular_formula!(N 1 H 3)
1514-
)]))
1529+
Ok((
1530+
4..4,
1531+
vec![NeutralLoss::Gain(1, molecular_formula!(N 1 H 3))]
1532+
))
15151533
);
15161534
assert_eq!(
15171535
parse_neutral_loss(&Context::default(), "/-0.0008", 0..8),

‎mzannotate/src/mzspeclib/analyte.rs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -128,7 +128,7 @@ impl AnalyteTarget {
128128
Self::Unknown(_) => None,
129129
Self::MolecularFormula(f) => Some(f.clone()),
130130
Self::PeptidoformIon(pep) => (pep.formulas()
131-
+ pep.get_charge_carriers().map(|m| m.formula()).unwrap_or_default())
131+
+ pep.get_charge_carriers().map(Molecule::formula).unwrap_or_default())
132132
.to_vec()
133133
.into_iter()
134134
.exactly_one()

‎mzannotate/src/mzspeclib/protein_description.rs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -245,7 +245,7 @@ impl ProteinDescription {
245245
}
246246
}
247247
curie!(MS:1003212) => {
248-
self.set_names.push(attribute.value.scalar().to_string().into_boxed_str())
248+
self.set_names.push(attribute.value.scalar().to_string().into_boxed_str());
249249
}
250250
curie!(MS:1000885) => {
251251
let string = attribute.value.scalar().to_string();

‎mzannotate/src/peptidoform.rs‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -94,10 +94,10 @@ pub(crate) fn generate_theoretical_fragments_inner<Complexity, Mode: MassOutputM
9494
peptidoform_index: usize,
9595
all_peptides: &[Peptidoform<Linked>],
9696
) -> Vec<Fragment<Mode>> {
97-
let default_charge = max_charge.map(|c| MolecularCharge::proton(c));
97+
let default_charge = max_charge.map(MolecularCharge::proton);
9898
let mut charge_carriers: Option<CachedCharge> = default_charge
9999
.as_ref()
100-
.map(|c| CachedCharge::from(peptidoform.get_charge_carriers().unwrap_or(&c)));
100+
.map(|c| CachedCharge::from(peptidoform.get_charge_carriers().unwrap_or(c)));
101101

102102
let mut output: Vec<Fragment<Mode>> =
103103
Vec::with_capacity(20 * peptidoform.sequence().len() + 75); // Empirically derived required size of the buffer (Derived from Hecklib)
@@ -226,7 +226,7 @@ pub(crate) fn generate_theoretical_fragments_inner<Complexity, Mode: MassOutputM
226226
for c in n..(peptidoform.len() - 1).min(*internal_range.end() + 1) {
227227
let o_n = options[n];
228228
let o_c = options[c];
229-
if !(o_c.0 || o_c.1 || o_c.2) && !(o_n.3 || o_n.4 || o_n.5) {
229+
if !(o_c.0 || o_c.1 || o_c.2 || o_n.3 || o_n.4 || o_n.5) {
230230
continue;
231231
}
232232

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