Updated rustyms and prepared for new version

Signed-off-by: Douwe Schulte <[email protected]>

.github/workflows/release.yml

@@ -35,7 +35,6 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           TAURI_PRIVATE_KEY: ${{ secrets.TAURI_PRIVATE_KEY }}
-          TAURI_KEY_PASSWORD: ${{ secrets.TAURI_KEY_PASSWORD }}
         with:
           tagName: v__VERSION__
           releaseName: 'Version __VERSION__'

src-tauri/Cargo.toml

@@ -6,7 +6,7 @@ authors = ["Douwe Schulte <[email protected]>"]
 license = "MIT OR Apache-2.0"
 repository = "https://github.com/snijderlab/annotator"
 edition = "2021"
-rust-version = "1.57"
+rust-version = "1.70.0"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
@@ -19,7 +19,7 @@ itertools = "0.12"
 serde_json = "1.0"
 serde = { version = "1.0", features = ["derive"] }
 tauri = { version = "1.6", features = ["shell-open", "dialog-open", "updater"] }
-rustyms = { path = "../../rustyms/rustyms", default-features = false, features = [
+rustyms = { version = "0.8.3", default-features = false, features = [
     "identification",
     "align",
 ] }

src-tauri/build.rs

@@ -1,6 +1,5 @@
 use std::io::Write;
 use std::{fs::File, io::BufWriter};
-use tauri;
 
 fn create_loss_modal(id: &str) -> String {
     format!(

src-tauri/src/main.rs

@@ -264,7 +264,7 @@ async fn search_modification(text: &str, tolerance: f64) -> Result<String, Strin
                     .map(|(ontology, id, _, modification)| {
                         [
                             modification.to_string(),
-                            format!("{}:{}", ontology.name(), id),
+                            format!("<a onclick='document.getElementById(\"search-modification\").value=\"{0}:{1}\";document.getElementById(\"search-modification-button\").click()'>{0}:{1}</a>", ontology.name(), id),
                             display_mass(modification.formula().monoisotopic_mass()).to_string(),
                             format!(
                                 "<span class='formula'>{}</span>",
@@ -284,21 +284,20 @@ async fn search_modification(text: &str, tolerance: f64) -> Result<String, Strin
                     .map(|(ontology, id, _, modification)| {
                         [
                             modification.to_string(),
-                            format!("{}:{}", ontology.name(), id),
+                            format!("<a onclick='document.getElementById(\"search-modification\").value=\"{0}:{1}\";document.getElementById(\"search-modification-button\").click()'>{0}:{1}</a>", ontology.name(), id),
                         ]
                     })
                     .collect_vec(),
             )
             .to_string())
         }
         ModificationSearchResult::Glycan(_, modifications) => Ok(html_builder::HtmlElement::table(
-            Some(&["Name", "Id", "Structure"]),
+            Some(&["Name", "Structure"]),
             &modifications
                 .iter()
-                .map(|(ontology, id, _, modification)| {
+                .map(|(_, _, _, modification)| {
                     [
-                        modification.to_string(),
-                        format!("{}:{}", ontology.name(), id),
+                        format!("<a onclick='document.getElementById(\"search-modification\").value=\"{0}\";document.getElementById(\"search-modification-button\").click()'>{0}</a>", modification),
                         if let Modification::Gno(GnoComposition::Structure(structure), _) =
                             modification
                         {
@@ -408,7 +407,6 @@ fn spectrum_details(index: usize, state: ModifiableState) -> String {
 
 #[tauri::command]
 fn identified_peptide_details(index: usize, state: ModifiableState) -> String {
-    // TODO: show local confidence on the sequence (maybe as done in stitch before?)
     state.lock().unwrap().peptides.get(index).map_or(
         "Identified peptide index not valid".to_string(),
         |peptide| peptide.to_html().to_string(),

src-tauri/src/render.rs

@@ -670,65 +670,11 @@ fn render_linear_peptide(
         write!(output, "<span class='modification term'></span>").unwrap();
     }
     if let Some(charge_carriers) = &peptide.charge_carriers {
-        // TODO: When rustyms is updated use the display impl here
-        write!(output, "<span class='charge-carriers'>/",).unwrap();
         write!(
             output,
-            "{}",
-            charge_carriers
-                .charge_carriers
-                .iter()
-                .map(|c| c.0)
-                .sum::<isize>()
+            "<span class='charge-carriers'>/{charge_carriers}</span>",
         )
         .unwrap();
-        if !charge_carriers.charge_carriers.iter().all(|c| {
-            c.1 == MolecularFormula::new(&[(Element::H, None, 1), (Element::Electron, None, -1)])
-                .unwrap()
-        }) {
-            write!(output, "[").unwrap();
-            let mut first = true;
-            for (amount, formula) in &charge_carriers.charge_carriers {
-                if first {
-                    first = false;
-                } else {
-                    write!(output, ",").unwrap();
-                }
-                let electron_index = formula
-                    .elements()
-                    .iter()
-                    .position(|el| el.0 == Element::Electron);
-                let charge = electron_index.map(|ei| match -formula.elements()[ei].2 {
-                    1 => "+".to_string(),
-                    -1 => "-".to_string(),
-                    n => n.to_string(),
-                });
-                if let (Some(electron_index), Some(charge), 2) =
-                    (electron_index, &charge, formula.elements().len())
-                {
-                    let element_index = 1 - electron_index;
-                    write!(
-                        output,
-                        "{}{}{}",
-                        amount,
-                        formula.elements()[element_index].0,
-                        charge
-                    )
-                    .unwrap();
-                } else {
-                    write!(
-                        output,
-                        "{}({}){}",
-                        amount,
-                        formula,
-                        charge.unwrap_or_default()
-                    )
-                    .unwrap();
-                }
-            }
-            write!(output, "]").unwrap();
-        }
-        write!(output, "</span>").unwrap();
     }
     write!(output, "</div>").unwrap();
 }

src-tauri/tauri.conf.json

@@ -67,7 +67,7 @@
         "https://gist.github.com/douweschulte/4afc3cac1a8f12473b281ac4e255e636"
       ],
       "dialog": true,
-      "pubkey": "dW50cnVzdGVkIGNvbW1lbnQ6IG1pbmlzaWduIHB1YmxpYyBrZXk6IEUyRjQ4NDA2MEU5NkNGOUQKUldTZHo1WU9Cb1QwNG1URkMwdUNtL0xKVjczSUNXbTZRWUE2K2QzUk96U0xXcTFLVGtuSGp3QWcK"
+      "pubkey": "dW50cnVzdGVkIGNvbW1lbnQ6IG1pbmlzaWduIHB1YmxpYyBrZXk6IEJGQTVFRjQwREVERjBBRjkKUldUNUN0L2VRTytsdjhrSjRDY1ZWVlNCOFNYV292anozRXZyZDR0eC95c3FMRWtjdWM1MHpIczIK"
     },
     "windows": [
       {