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Slight refactorings
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@douweschulte
douweschulte committed Oct 30, 2023
1 parent fe66332 commit 22a62c9
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Showing 3 changed files with 75 additions and 56 deletions.
18 changes: 9 additions & 9 deletions src-tauri/build.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,6 @@ r#"<!DOCTYPE html>
</div>
</div>
<pre id="spectrum-details"></pre>
<div class="input-settings">
<label for="spectrum-index">Identified peptide index</label>
<div class="combined-input">
<input type="number" id="details-identified-peptide-index" value="0" min="0" />
<span>/</span>
<span id="number-of-identified-peptides">0</span>
</div>
<button id="load-identified-peptide" type="button">Load identified peptide</button>
</div>
<div class="input-settings">
<label for="search-peptide-input">Search peptide</label>
<div class="combined-input">
Expand All @@ -60,6 +51,15 @@ r#"<!DOCTYPE html>
</div>
</div>
<div id="resulting-peptides"></div>
<div class="input-settings">
<label for="spectrum-index">Identified peptide index</label>
<div class="combined-input">
<input type="number" id="details-identified-peptide-index" value="0" min="0" />
<span>/</span>
<span id="number-of-identified-peptides">0</span>
</div>
<button id="load-identified-peptide" type="button">Load identified peptide</button>
</div>
<div id="identified-peptide-details"></div>
<pre id="loaded-path"></pre>
<div class="input-settings">
Expand Down
7 changes: 7 additions & 0 deletions src-tauri/src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,12 @@ mod state;

type ModifiableState<'a> = tauri::State<'a, std::sync::Mutex<State>>;

#[tauri::command]
fn refresh(state: ModifiableState) -> (usize, usize) {
let state = state.lock().unwrap();
(state.spectra.len(), state.peptides.len())
}

#[tauri::command]
async fn load_mgf<'a>(path: &'a str, state: ModifiableState<'a>) -> Result<usize, String> {
match rustyms::rawfile::mgf::open(path) {
Expand Down Expand Up @@ -404,6 +410,7 @@ fn main() {
peptides: Vec::new(),
}))
.invoke_handler(tauri::generate_handler![
refresh,
load_mgf,
load_identified_peptides,
load_clipboard,
Expand Down
106 changes: 59 additions & 47 deletions src/main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,10 @@ async function select_mgf_file(e) {
extensions: ['mgf', 'mgf.gz'], name: "*"
}]
};
e.dataset.filepath = await window.__TAURI__.dialog.open(properties);
load_mgf(e);
window.__TAURI__.dialog.open(properties).then((result) => {
e.dataset.filepath = result;
load_mgf(e);
})
};

/**
Expand All @@ -28,8 +30,10 @@ async function select_identified_peptides_file(e) {
extensions: ["csv", "csv.gz", "psmtsv", "psmtsv.gz", "fasta", "fasta.gz"], name: "*"
}]
};
e.dataset.filepath = await window.__TAURI__.dialog.open(properties);
load_identified_peptides(e);
window.__TAURI__.dialog.open(properties).then((result) => {
e.dataset.filepath = result;
load_identified_peptides(e);
})
};

/**
Expand Down Expand Up @@ -76,48 +80,46 @@ async function load_clipboard() {
navigator.clipboard
.readText()
.then(async (clipText) => {
try {
let result = await invoke("load_clipboard", { data: clipText });
invoke("load_clipboard", { data: clipText }).then((result) => {
document.querySelector("#spectrum-log").innerText = "Loaded " + result + " spectra";
document.querySelector("#loaded-path").classList.remove("error");
document.querySelector("#loaded-path").innerText = "Clipboard";
document.querySelector("#number-of-scans").innerText = result;
spectrum_details();
} catch (error) {
}).catch((error) => {
document.querySelector("#load-clipboard").classList.remove("loading")
console.log(error);
document.querySelector("#loaded-path").classList.add("error");
document.querySelector("#loaded-path").innerText = error;
}
document.querySelector("#load-clipboard").classList.remove("loading")
document.querySelector("#load-clipboard").classList.remove("loading")
})
});
}

async function spectrum_details() {
try {
let result = await invoke("spectrum_details", { index: Number(document.querySelector("#details-spectrum-index").value) });
document.querySelector("#spectrum-details").innerText = result;
} catch (error) {
invoke("spectrum_details", { index: Number(document.querySelector("#details-spectrum-index").value) }).then(
(result) => document.querySelector("#spectrum-details").innerText = result
).catch((error) => {
console.log(error);
document.querySelector("#spectrum-error").classList.remove("hidden");
document.querySelector("#spectrum-error").innerText = error;
document.querySelector("#spectrum-details").innerText = "ERROR";
}
})
}

let displayed_identified_peptide = undefined;
async function identified_peptide_details() {
try {
let index = Number(document.querySelector("#details-identified-peptide-index").value);
if (displayed_identified_peptide != index) {
let result = await invoke("identified_peptide_details", { index: index });
let index = Number(document.querySelector("#details-identified-peptide-index").value);
if (displayed_identified_peptide != index) {
invoke("identified_peptide_details", { index: index }).then((result) => {
document.querySelector("#identified-peptide-details").innerHTML = result;
displayed_identified_peptide = index;
}
} catch (error) {
console.log(error);
document.querySelector("#spectrum-error").classList.remove("hidden");
document.querySelector("#spectrum-error").innerText = error;
document.querySelector("#identified-peptide-details").innerText = "ERROR";
}).catch((error) => {
console.log(error);
document.querySelector("#spectrum-error").classList.remove("hidden");
document.querySelector("#spectrum-error").innerText = error;
document.querySelector("#identified-peptide-details").innerText = "ERROR";
})
}
}

Expand All @@ -140,20 +142,19 @@ async function search_peptide() {
}

async function load_identified_peptide() {
try {
let index = Number(document.querySelector("#details-identified-peptide-index").value);
let result = await invoke("load_identified_peptide", { index: index });
let index = Number(document.querySelector("#details-identified-peptide-index").value);
invoke("load_identified_peptide", { index: index }).then((result) => {
document.querySelector("#peptide").innerText = result.peptide;
document.querySelector("#spectrum-charge").value = result.charge;
document.querySelector("#spectrum-model").value = result.mode.toLowerCase();
document.querySelector("#details-spectrum-index").value = result.scan_index;
console.log(result)
} catch (error) {
}).catch((error) => {
console.log(error);
document.querySelector("#spectrum-error").classList.remove("hidden");
document.querySelector("#spectrum-error").innerText = error;
document.querySelector("#identified-peptide-details").innerText = "ERROR";
}
})
}


Expand All @@ -180,38 +181,37 @@ function get_location(id) {
async function annotate_spectrum() {
document.querySelector("#annotate-button").classList.add("loading");
document.querySelector("#peptide").innerText = document.querySelector("#peptide").innerText.trim();
try {
var charge = document.querySelector("#spectrum-charge").value == "" ? null : Number(document.querySelector("#spectrum-charge").value);
var noise_threshold = document.querySelector("#noise-threshold").value == "" ? null : Number(document.querySelector("#noise-threshold").value);
var model = [
[get_location("#model-a-location"), document.querySelector("#model-a-loss").value],
[get_location("#model-b-location"), document.querySelector("#model-b-loss").value],
[get_location("#model-c-location"), document.querySelector("#model-c-loss").value],
[get_location("#model-d-location"), document.querySelector("#model-d-loss").value],
[get_location("#model-v-location"), document.querySelector("#model-v-loss").value],
[get_location("#model-w-location"), document.querySelector("#model-w-loss").value],
[get_location("#model-x-location"), document.querySelector("#model-x-loss").value],
[get_location("#model-y-location"), document.querySelector("#model-y-loss").value],
[get_location("#model-z-location"), document.querySelector("#model-z-loss").value],
[get_location("#model-z-location"), document.querySelector("#model-precursor-loss").value], // First element is discarded
];
var result = await invoke("annotate_spectrum", { index: Number(document.querySelector("#details-spectrum-index").value), ppm: Number(document.querySelector("#spectrum-ppm").value), charge: charge, noise_threshold: noise_threshold, model: document.querySelector("#spectrum-model").value, peptide: document.querySelector("#peptide").innerText, cmodel: model });
var charge = document.querySelector("#spectrum-charge").value == "" ? null : Number(document.querySelector("#spectrum-charge").value);
var noise_threshold = document.querySelector("#noise-threshold").value == "" ? null : Number(document.querySelector("#noise-threshold").value);
var model = [
[get_location("#model-a-location"), document.querySelector("#model-a-loss").value],
[get_location("#model-b-location"), document.querySelector("#model-b-loss").value],
[get_location("#model-c-location"), document.querySelector("#model-c-loss").value],
[get_location("#model-d-location"), document.querySelector("#model-d-loss").value],
[get_location("#model-v-location"), document.querySelector("#model-v-loss").value],
[get_location("#model-w-location"), document.querySelector("#model-w-loss").value],
[get_location("#model-x-location"), document.querySelector("#model-x-loss").value],
[get_location("#model-y-location"), document.querySelector("#model-y-loss").value],
[get_location("#model-z-location"), document.querySelector("#model-z-loss").value],
[get_location("#model-z-location"), document.querySelector("#model-precursor-loss").value], // First element is discarded
];
invoke("annotate_spectrum", { index: Number(document.querySelector("#details-spectrum-index").value), ppm: Number(document.querySelector("#spectrum-ppm").value), charge: charge, noise_threshold: noise_threshold, model: document.querySelector("#spectrum-model").value, peptide: document.querySelector("#peptide").innerText, cmodel: model }).then((result) => {
document.querySelector("#spectrum-results-wrapper").innerHTML = result[0];
document.querySelector("#spectrum-fragments").innerHTML = result[1];
document.querySelector("#spectrum-log").innerText = result[2];
document.querySelector("#spectrum-error").innerText = "";
document.querySelector("#spectrum-wrapper").classList.remove("hidden"); // Remove hidden class if this is the first run
document.querySelector("#spectrum-error").classList.add("hidden");
SetUpSpectrumInterface();
} catch (error) {
}).catch((error) => {
console.log(error);
document.querySelector("#spectrum-error").classList.remove("hidden");
document.querySelector("#spectrum-error").innerHTML = "<p class='title'>" + error.short_description + "</p><p class='description'>" + error.long_description + "</p>";
if (error.context.hasOwnProperty('Line')) {
let Line = error.context.Line;
document.querySelector("#peptide").innerHTML = Line.line.slice(0, Line.offset) + "<span class='error'>" + Line.line.slice(Line.offset, Line.offset + Line.length) + "</span>" + Line.line.slice(Line.offset + Line.length, Line.line.length);
}
}
})
document.querySelector("#annotate-button").classList.remove("loading");
}

Expand Down Expand Up @@ -250,4 +250,16 @@ window.addEventListener("DOMContentLoaded", () => {
.addEventListener("focus", (event) => {
event.target.innerHTML = event.target.innerText;
});

// Refresh interface for hot reload
invoke("refresh").then((result) => {
document.querySelector("#number-of-scans").innerText = result[0];
if (result[0] > 0) {
spectrum_details();
}
document.querySelector("#number-of-identified-peptides").innerText = result[1];
if (result[1] > 0) {
identified_peptide_details();
}
})
});

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