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Updated to new rustyms and version bump
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@douweschulte
douweschulte committed Jan 20, 2025
1 parent ea05847 commit aedfa12
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Showing 10 changed files with 186 additions and 160 deletions.
2 changes: 1 addition & 1 deletion backend/Cargo.lock
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2 changes: 1 addition & 1 deletion backend/Cargo.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[package]
name = "annotator"
version = "0.2.2"
version = "1.0.0"
description = "Spectrum annotator"
authors = ["Douwe Schulte <[email protected]>"]
license = "MIT OR Apache-2.0"
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2 changes: 1 addition & 1 deletion backend/src/identified_peptides.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ pub async fn search_peptide<'a>(
Context::None,
)
})?;
let search = LinearPeptide::<Linked>::pro_forma(text, Some(&state.database))?
let search = Peptidoform::<Linked>::pro_forma(text, Some(&state.database))?
.into_simple_linear()
.ok_or_else(|| {
CustomError::error(
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8 changes: 4 additions & 4 deletions backend/src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -315,12 +315,12 @@ async fn annotate_spectrum<'a>(
"most_abundant" => MassMode::MostAbundant,
_ => return Err(CustomError::error("Invalid mass mode", "", Context::None)),
};
let peptide = rustyms::CompoundPeptidoform::pro_forma(peptide, Some(&state.database))?;
let multiple_peptidoforms = peptide.peptidoforms().len() == 1;
let peptide = rustyms::CompoundPeptidoformIon::pro_forma(peptide, Some(&state.database))?;
let multiple_peptidoforms = peptide.peptidoform_ions().len() == 1;
let multiple_peptides = peptide
.peptidoforms()
.peptidoform_ions()
.iter()
.flat_map(|p| p.peptides())
.flat_map(|p| p.peptidoforms())
.count()
== 1;

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4 changes: 2 additions & 2 deletions backend/src/metadata_render.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,8 @@ impl RenderToHtml for IdentifiedPeptide {
.map(|p| format!("{}&nbsp;AA", match p {
ReturnedPeptide::LinearSemiAmbiguous(p) => p.len().to_string(),
ReturnedPeptide::LinearSimpleLinear(p) => p.len().to_string(),
ReturnedPeptide::Peptidoform(p) => p.peptides().iter().map(|p| p.len()).join("&nbsp;+&nbsp;"),
ReturnedPeptide::CompoundPeptidoform(p) => p.peptides().map(|p| p.len()).join("&nbsp;+&nbsp;"),
ReturnedPeptide::Peptidoform(p) => p.peptidoforms().iter().map(|p| p.len()).join("&nbsp;+&nbsp;"),
ReturnedPeptide::CompoundPeptidoform(p) => p.peptidoforms().map(|p| p.len()).join("&nbsp;+&nbsp;"),
}))
.to_optional_string(),
formula
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110 changes: 60 additions & 50 deletions backend/src/render/all.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ use rustyms::{
placement_rule::PlacementRule,
spectrum::{AnnotatedPeak, Fdr, PeakSpectrum, Recovered, Score},
system::{da, mz, Mass, MassOverCharge},
AnnotatedSpectrum, CompoundPeptidoform, MassMode, Model, MolecularFormula, NeutralLoss,
AnnotatedSpectrum, CompoundPeptidoformIon, MassMode, Model, MolecularFormula, NeutralLoss,
};

use crate::{
Expand All @@ -33,17 +33,17 @@ pub fn annotated_spectrum(
let (limits, overview) = get_overview(spectrum);
let (graph_data, graph_boundaries) =
spectrum_graph_boundaries(spectrum, fragments, model, mass_mode);
let multiple_peptidoforms = spectrum.peptide.peptidoforms().len() > 1;
let multiple_peptides = spectrum
let multiple_peptidoform_ions = spectrum.peptide.peptidoform_ions().len() > 1;
let multiple_peptidoforms = spectrum
.peptide
.peptidoforms()
.peptidoform_ions()
.iter()
.any(|p| p.peptides().len() > 1);
.any(|p| p.peptidoforms().len() > 1);
let multiple_glycans = spectrum
.peptide
.peptidoforms()
.peptidoform_ions()
.iter()
.flat_map(|p| p.peptides())
.flat_map(|p| p.peptidoforms())
.any(|p| {
p.sequence()
.iter()
Expand Down Expand Up @@ -72,8 +72,8 @@ pub fn annotated_spectrum(
&graph_boundaries,
&limits,
"first",
multiple_peptidoform_ions,
multiple_peptidoforms,
multiple_peptides,
multiple_glycans,
mass_mode,
&unique_peptide_lookup,
Expand All @@ -93,8 +93,8 @@ pub fn annotated_spectrum(
&mut output,
spectrum,
fragments,
multiple_peptidoform_ions,
multiple_peptidoforms,
multiple_peptides,
model,
mass_mode,
);
Expand Down Expand Up @@ -413,10 +413,10 @@ pub struct Limits {
fn get_overview(spectrum: &AnnotatedSpectrum) -> (Limits, PositionCoverage) {
let mut output: PositionCoverage = spectrum
.peptide
.peptidoforms()
.peptidoform_ions()
.iter()
.map(|p| {
p.peptides()
p.peptidoforms()
.iter()
.map(|p| vec![HashMap::new(); p.len()])
.collect()
Expand All @@ -433,7 +433,7 @@ fn get_overview(spectrum: &AnnotatedSpectrum) -> (Limits, PositionCoverage) {
peak.annotation.iter().for_each(|fragment| {
fragment.ion.position().map(|i| {
if let (Some(pii), Some(pi)) =
(fragment.peptidoform_index, fragment.peptide_index)
(fragment.peptidoform_ion_index, fragment.peptidoform_index)
{
*output[pii][pi][match i.sequence_index {
rustyms::SequencePosition::Index(i) => i,
Expand Down Expand Up @@ -608,20 +608,21 @@ fn render_spectrum(
pub fn spectrum_table(
spectrum: &AnnotatedSpectrum,
fragments: &[Fragment],
multiple_peptidoform_ions: bool,
multiple_peptidoforms: bool,
multiple_peptides: bool,
) -> String {
fn generate_text(
annotation: &Fragment,
compound_peptidoform: &CompoundPeptidoform,
compound_peptidoform: &CompoundPeptidoformIon,
) -> (String, String, String) {
if let Some(pos) = annotation.ion.position() {
(
format!(
"{}{}",
compound_peptidoform.peptidoforms()
[annotation.peptidoform_index.unwrap_or_default()]
.peptides()[annotation.peptide_index.unwrap_or_default()][pos.sequence_index]
compound_peptidoform.peptidoform_ions()
[annotation.peptidoform_ion_index.unwrap_or_default()]
.peptidoforms()[annotation.peptidoform_index.unwrap_or_default()]
[pos.sequence_index]
.aminoacid
.char(),
display_sequence_index(pos.sequence_index)
Expand Down Expand Up @@ -696,12 +697,12 @@ pub fn spectrum_table(
<th>Additional label</th>
</tr></thead><tdata>",
spectrum.peptide,
if multiple_peptidoforms {
if multiple_peptidoform_ions {
"<th>Peptidoform</th>"
} else {
""
},
if multiple_peptides {
if multiple_peptidoforms {
"<th>Peptide</th>"
} else {
""
Expand Down Expand Up @@ -742,16 +743,16 @@ pub fn spectrum_table(
peak.experimental_mz.value,
[
"matched".to_string(),
if multiple_peptidoforms {
if multiple_peptidoform_ions {
annotation
.peptidoform_index
.peptidoform_ion_index
.map_or("?".to_string(), |i| (i + 1).to_string())
} else {
String::new()
},
if multiple_peptides {
if multiple_peptidoforms {
annotation
.peptide_index
.peptidoform_index
.map_or("?".to_string(), |i| (i + 1).to_string())
} else {
String::new()
Expand Down Expand Up @@ -804,16 +805,16 @@ pub fn spectrum_table(
.map_or(f64::NAN, |v| v.value),
[
"fragment".to_string(),
if multiple_peptidoforms {
if multiple_peptidoform_ions {
fragment
.peptidoform_index
.map_or("?".to_string(), |i| (i + 1).to_string())
} else {
String::new()
},
if multiple_peptides {
if multiple_peptidoforms {
fragment
.peptide_index
.peptidoform_index
.map_or("?".to_string(), |i| (i + 1).to_string())
} else {
String::new()
Expand Down Expand Up @@ -848,8 +849,8 @@ pub fn spectrum_table(
data.sort_unstable_by(|a, b| a.0.total_cmp(&b.0));
for row in data {
write!(output, "<tr class='{}'>", row.1[0]).unwrap();
for cell in &row.1[if multiple_peptides {
if multiple_peptidoforms {
for cell in &row.1[if multiple_peptidoforms {
if multiple_peptidoform_ions {
1
} else {
2
Expand All @@ -870,8 +871,8 @@ fn general_stats(
output: &mut String,
spectrum: &AnnotatedSpectrum,
fragments: &[Fragment],
multiple_peptidoform_ions: bool,
multiple_peptidoforms: bool,
multiple_peptides: bool,
model: &Model,
mass_mode: MassMode,
) {
Expand Down Expand Up @@ -944,17 +945,19 @@ fn general_stats(
let (combined_scores, separate_peptide_scores) = spectrum.scores(fragments, model, mass_mode);
let fdr = (spectrum.spectrum().len() != 0).then(|| spectrum.fdr(fragments, model, mass_mode));

for (peptidoform_index, peptidoform_scores) in separate_peptide_scores.iter().enumerate() {
for (peptide_index, peptide_score) in peptidoform_scores.iter().enumerate() {
let precursor = spectrum.peptide.peptidoforms()[peptidoform_index].peptides()
[peptide_index]
for (peptidoform_ion_index, peptidoform_ion_scores) in
separate_peptide_scores.iter().enumerate()
{
for (peptidoform_index, peptidoform_score) in peptidoform_ion_scores.iter().enumerate() {
let precursor = spectrum.peptide.peptidoform_ions()[peptidoform_ion_index]
.peptidoforms()[peptidoform_index]
.clone()
.into_linear()
.map_or("Part of peptidoform".to_string(), |p| {
.map_or("Part of peptidoform ion".to_string(), |p| {
p.formulas().iter().map(display_masses).join(", ")
});
write!(mass_row, "<td>{precursor}</td>").unwrap();
match peptide_score.score {
match peptidoform_score.score {
Score::Position {
fragments,
peaks,
Expand All @@ -976,7 +979,7 @@ fn general_stats(
"<td>{}</td>",
fdr.as_ref()
.map(|(_, separate_peptide_fdrs)| format_fdr_peaks(
&separate_peptide_fdrs[peptidoform_index][peptide_index]
&separate_peptide_fdrs[peptidoform_ion_index][peptidoform_index]
))
.to_optional_string()
)
Expand All @@ -986,7 +989,7 @@ fn general_stats(
"<td>{}</td>",
fdr.as_ref()
.map(|(_, separate_peptide_fdrs)| format_fdr_intensity(
&separate_peptide_fdrs[peptidoform_index][peptide_index]
&separate_peptide_fdrs[peptidoform_ion_index][peptidoform_index]
))
.to_optional_string()
)
Expand All @@ -1012,7 +1015,7 @@ fn general_stats(
"<td>{}</td>",
fdr.as_ref()
.map(|(_, separate_peptide_fdrs)| format_fdr_peaks(
&separate_peptide_fdrs[peptidoform_index][peptide_index]
&separate_peptide_fdrs[peptidoform_ion_index][peptidoform_index]
))
.to_optional_string()
)
Expand All @@ -1022,7 +1025,7 @@ fn general_stats(
"<td>{}</td>",
fdr.as_ref()
.map(|(_, separate_peptide_fdrs)| format_fdr_intensity(
&separate_peptide_fdrs[peptidoform_index][peptide_index]
&separate_peptide_fdrs[peptidoform_ion_index][peptidoform_index]
))
.to_optional_string()
)
Expand All @@ -1033,7 +1036,7 @@ fn general_stats(
write!(peaks_details_row, "<td><table>").unwrap();
write!(intensity_details_row, "<td><table>").unwrap();
write!(positions_details_row, "<td><table>").unwrap();
for (ion, score) in &peptide_score.ions {
for (ion, score) in &peptidoform_score.ions {
match score {
Score::Position {
fragments,
Expand Down Expand Up @@ -1108,22 +1111,29 @@ fn general_stats(
}

write!(output, "<label><input type='checkbox' switch id='general-stats-show-details'>Show statistics per ion series</label><table class='general-stats'>").unwrap();
if multiple_peptidoforms || multiple_peptides {
if multiple_peptidoform_ions || multiple_peptidoforms {
write!(output, "<tr><td>General Statistics</td>").unwrap();
for (peptidoform_index, peptidoform) in spectrum.peptide.peptidoforms().iter().enumerate() {
for peptide_index in 0..peptidoform.peptides().len() {
if multiple_peptidoforms && multiple_peptides {
for (peptidoform_ion_index, peptidoform_ion) in
spectrum.peptide.peptidoform_ions().iter().enumerate()
{
for peptidoform_index in 0..peptidoform_ion.peptidoforms().len() {
if multiple_peptidoform_ions && multiple_peptidoforms {
write!(
output,
"<td>Peptidoform ion {} Peptidoform {}</td>",
peptidoform_ion_index + 1,
peptidoform_index + 1
)
.unwrap();
} else if multiple_peptidoform_ions {
write!(
output,
"<td>Peptidoform {} Peptide {}</td>",
peptidoform_index + 1,
peptide_index + 1
"<td>Peptidoform ion {} </td>",
peptidoform_ion_index + 1,
)
.unwrap();
} else if multiple_peptidoforms {
write!(output, "<td>Peptidoform {} </td>", peptidoform_index + 1,).unwrap();
} else if multiple_peptides {
write!(output, "<td>Peptide {}</td>", peptide_index + 1).unwrap();
write!(output, "<td>Peptidoform {}</td>", peptidoform_index + 1).unwrap();
}
}
}
Expand Down
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