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use std::ops::Range;
use context_error::*;
use crate::{
ParserResult,
chemistry::{MolecularFormula, Molecule},
glycan::{GLYCAN_PARSE_LIST, MonoSaccharide},
helper_functions::{explain_number_error, next_number, str_starts_with},
};
/// All possible errors when parsing a ProForma glycan composition
#[derive(Clone, Copy, Debug, Default, Eq, PartialEq)]
pub enum GlycanCompositionError {
/// A missing closing brackets for a formula '}'
NoClosingBracket,
/// A name was used that is not defined
UnrecognisedName,
/// An invalid occurrence number was specified
InvalidNumber,
/// An invalid formula was given for a custom monosaccharide
InvalidFormula,
/// Some monosaccharide occurrence was outside of bounds for [`isize`]
OutOfRangeOccurance,
/// An empty composition was given, this also includes cases where monosaccharides cancel each
/// other out like `Hex2Hex-2`
#[default]
Empty,
/// A synonym was given (will only be checked in strict mode)
ImproperName,
/// A name was given with improper capitalisation (will only be checked in strict mode)
ImproperCapitalisation,
/// The occurrence was missing for a glycan, this is always generated because it might mean that
/// the composition was parsed as something not intended by the user
ImproperMissingOccurance,
/// The sign was missing for a mass custom monosaccharide, eg `{203}` instead of `{+203}`
ImproperMissingSign,
}
impl ErrorKind for GlycanCompositionError {
type Settings = ();
fn descriptor(&self) -> &'static str {
match self {
Self::ImproperCapitalisation | Self::ImproperMissingOccurance | Self::ImproperName => {
"warning"
}
_ => "error",
}
}
fn ignored(&self, _settings: Self::Settings) -> bool {
false
}
fn is_error(&self, _settings: Self::Settings) -> bool {
!matches!(
self,
Self::ImproperCapitalisation | Self::ImproperMissingOccurance | Self::ImproperName
)
}
}
impl From<GlycanCompositionError> for BasicKind {
fn from(value: GlycanCompositionError) -> Self {
if value.is_error(()) {
Self::Error
} else {
Self::Warning
}
}
}
impl MonoSaccharide {
/// Parse the given text as a ProForma glycan composition.
/// ```rust
/// use mzcore::glycan::MonoSaccharide;
/// assert!(
/// MonoSaccharide::pro_forma_composition::<false>(
/// "HexNAc5Hex3Fuc1"
/// )
/// .is_ok()
/// );
/// assert!(
/// MonoSaccharide::pro_forma_composition::<false>(
/// "HexNAc4Hex5Fuc1NeuAc1{C8H13N1O5Na1:z+1}1"
/// )
/// .is_ok()
/// );
/// ```
/// # Errors
/// When the composition could not be read. Or when any of the glycans numbers outside of the
/// valid numerical range. Warns when the amount is missing.
pub fn pro_forma_composition<const STRICT: bool>(
value: &str,
) -> ParserResult<'_, Vec<(Self, isize)>, GlycanCompositionError> {
Self::pro_forma_composition_inner::<STRICT>(
&Context::default().lines(0, value),
value,
0..value.len(),
)
}
/// Parse the given text as a ProForma glycan composition.
/// # Errors
/// When the composition could not be read. Or when any of the glycans numbers outside of the
/// valid numerical range. Warns when the amount is missing.
pub fn pro_forma_composition_inner<'a, const STRICT: bool>(
base_context: &Context<'a>,
line: &'a str,
range: Range<usize>,
) -> ParserResult<'a, Vec<(Self, isize)>, GlycanCompositionError> {
let mut index = range.start;
let mut errors = Vec::new();
let end = line.len().min(range.end);
let mut output = Vec::new();
while index < end {
let start_glycan = index;
let sugar = if line[index..end].starts_with(' ') {
index += 1;
continue;
} else if line[index..end].starts_with('{') {
let end_formula = handle!(single errors, line[index + 1..end].find('}').ok_or_else(||BoxedError::new(
GlycanCompositionError::NoClosingBracket,
"Invalid ProForma glycan",
"The custom formula is not closed. No closing bracket '}' could be found.",
base_context.clone().add_highlight((0, index..end)),
)));
let ms = if let Ok(num) = line[index + 1..index + 1 + end_formula].parse::<f64>() {
if line[index + 1..].starts_with('+') && line[index + 1..].starts_with('-') {
errors.push(BoxedError::new(
GlycanCompositionError::ImproperMissingSign,
"Improper modification",
"A numerical modification should always be specified with a sign (+/-) to help it be recognised as a mass modification and not a modification index.",
base_context
.clone()
.add_highlight((0, index+1, 1)),
));
}
Self::new(
crate::glycan::BaseSugar::Custom(Box::new(
MolecularFormula::with_additional_mass(num),
)),
&[],
)
} else {
let formula = handle!(single errors,
MolecularFormula::pro_forma_inner::<true, false>(base_context, line, index + 1..index + 1+end_formula).map_err(|e| e.convert(|_| GlycanCompositionError::InvalidFormula)));
Self::new(crate::glycan::BaseSugar::Custom(formula.into()), &[])
};
index += end_formula + 2;
ms
} else {
let mut found = None;
'find_glycan: for (names, sugar) in GLYCAN_PARSE_LIST.iter() {
for name in names {
if str_starts_with::<true>(&line[index..end], name) {
found = Some(sugar.clone());
if STRICT {
let pro_forma_name = sugar.pro_forma_name();
if **name != pro_forma_name {
combine_error(
&mut errors,
BoxedError::new(
GlycanCompositionError::ImproperName,
"Improper ProForma glycan",
format!(
"While `{name}` can be unambiguously parsed the proper name in ProForma is `{pro_forma_name}`."
),
base_context.clone().add_highlight((
0,
index,
name.len(),
)),
),
);
} else if !line[index..end].starts_with(&**name) {
combine_error(
&mut errors,
BoxedError::new(
GlycanCompositionError::ImproperCapitalisation,
"Improper ProForma glycan",
"This glycan was not written with the proper capitalisation.",
base_context.clone().add_highlight((
0,
index,
name.len(),
)),
),
);
}
}
index += name.len();
break 'find_glycan;
}
}
}
handle!(single errors, found.ok_or_else(|| BoxedError::new(
GlycanCompositionError::UnrecognisedName,
"Invalid ProForma glycan",
"No valid glycan name could be recognised.",
base_context.clone().add_highlight((0, index..end)),
)))
};
let num = if let Some((offset, _, num)) =
next_number::<true, false, isize>(line, index..end)
{
index += offset;
handle!(single errors, num.map_err(|e| BoxedError::new(
GlycanCompositionError::InvalidNumber,
"Invalid ProForma glycan",
format!("The monosaccharide occurance number {}", explain_number_error(&e)),
base_context.clone().add_highlight((0, index-offset..index)),
)))
} else {
combine_error(
&mut errors,
BoxedError::new(
GlycanCompositionError::ImproperMissingOccurance,
"Improper ProForma glycan",
"No amount for this glycan was specified, it is assumed to occur once.",
base_context.clone().add_highlight((0, start_glycan..index)),
),
);
1
};
output.push((sugar, num));
}
let composition = handle!(single errors, Self::simplify_composition(output).ok_or_else(|| {
BoxedError::new(
GlycanCompositionError::OutOfRangeOccurance,
"Invalid ProForma glycan composition",
format!(
"The occurrence of a monosaccharide species is outside of the range {} to {}",
isize::MIN,
isize::MAX
),
base_context.clone().add_highlight((0, range.clone())),
)
}));
if let Some(f) = composition.iter().try_fold(MolecularFormula::default(), |acc, (s, n)| {
s.formula().checked_mul_isize(*n).and_then(|f| acc.checked_add(&f))
}) {
if composition.is_empty() || f.is_empty() {
combine_error(
&mut errors,
BoxedError::new(
GlycanCompositionError::Empty,
"Invalid ProForma glycan composition",
"The glycan composition is empty",
base_context.clone().add_highlight((0, range)),
),
);
Err(errors)
} else {
Ok((composition, errors))
}
} else {
combine_error(
&mut errors,
BoxedError::new(
GlycanCompositionError::OutOfRangeOccurance,
"Invalid ProForma glycan composition",
"The occurance of an element overflowed during calculation of the full molecular formula",
base_context.clone().add_highlight((0, range.clone())),
),
);
Err(errors)
}
}
/// Simplify a glycan composition to be sorted and deduplicated.
/// Returns None if overflow occurred, meaning that there where more than `isize::MAX` or less
/// then `isize::MIN` monosaccharides for one species.
pub(crate) fn simplify_composition(
mut composition: Vec<(Self, isize)>,
) -> Option<Vec<(Self, isize)>> {
// Sort on monosaccharide
composition.retain(|el| el.1 != 0 && !el.0.formula().is_empty());
composition.sort_unstable_by(|a, b| a.0.cmp(&b.0));
// Deduplicate
let mut max = composition.len().saturating_sub(1);
let mut index = 0;
while index < max {
let this = &composition[index];
let next = &composition[index + 1];
if this.0 == next.0 {
composition[index].1 = composition[index].1.checked_add(next.1)?;
composition.remove(index + 1);
max = max.saturating_sub(1);
} else {
index += 1;
}
}
composition.retain(|el| el.1 != 0);
Some(composition)
}
/// Parse the given text as a MSFragger glycan composition. Examples:
/// * HexNAc(5)Hex(3)Fuc(1)
/// * HexNAc(4)Hex(5)Fuc(1)NeuAc(1)
/// # Errors
/// When the composition could not be read. Or when any of the glycans occurs outside of the
/// valid range
pub fn byonic_composition(text: &str) -> Result<Vec<(Self, isize)>, BoxedError<'_, BasicKind>> {
let mut index = 0;
let mut output = Vec::new();
while index < text.len() {
if text[index..].starts_with(' ') {
index += 1;
} else if let Some(next_open_bracket) = text[index..].find('(') {
if let Some(next_close_bracket) = text[index + next_open_bracket..].find(')') {
let name = text[index..index + next_open_bracket].trim();
let mut sugar = None;
for option in GLYCAN_PARSE_LIST.as_slice() {
for o in &option.0 {
if o.eq_ignore_ascii_case(name) {
sugar = Some(option.1.clone());
break;
}
}
}
let number = text[index + next_open_bracket + 1
..index + next_open_bracket + next_close_bracket]
.trim()
.parse::<isize>();
output.push((
sugar.ok_or_else(|| {
BoxedError::new(
BasicKind::Error,
"Invalid MSFragger glycan composition",
"The sugar name could not be recognised",
Context::default().lines(0, text).add_highlight((
0,
index,
name.len(),
)),
)
})?,
number.map_err(|err| {
BoxedError::new(
BasicKind::Error,
"Invalid MSFragger glycan composition",
format!("Sugar count number is {}", explain_number_error(&err)),
Context::default().lines(0, text).add_highlight((
0,
index + next_open_bracket + 1,
next_close_bracket - 1,
)),
)
})?,
));
index += next_open_bracket + next_close_bracket + 1;
} else {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid MSFragger glycan composition",
"No closing bracket found ')'",
Context::default().lines(0, text).add_highlight((
0,
index + next_open_bracket,
1,
)),
));
}
} else if text[index..].chars().all(|c| c.is_ascii_whitespace()) {
break; // Allow trailing whitespace
} else {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid MSFragger glycan composition",
"No opening bracket found but there is text left, the format expected is 'Sugar(Number)'",
Context::default().lines(0, text).add_highlight((0, index, 1)),
));
}
}
Self::simplify_composition(output).ok_or_else(|| {
BoxedError::new(
BasicKind::Error,
"Invalid MSFragger glycan composition",
format!(
"The occurrence of one monosaccharide species is outside of the range {} to {}",
isize::MIN,
isize::MAX
),
Context::default().lines(0, text),
)
})
}
/// Display a composition as a ProForma glycan composition
pub fn display_composition(composition: &[(Self, isize)]) -> String {
composition
.iter()
.fold(String::new(), |acc, m| acc + &format!("{}{}", m.0, m.1))
}
}