protvista-uniprot 4.3.2 → 4.3.4

package/dist/protvista-uniprot.mjs

@@ -241,7 +241,9 @@ const Tm = {
     )
   ];
   let a;
-  const o = new Set(t.flatMap(({ name: s }) => s));
+  const o = new Set(
+    t.flatMap(({ name: s }) => s)
+  );
   return o.size && (o.size > 1 ? console.error(
     `PTMeXchange PTM has a mixture of modifications: ${Array.from(
       o
@@ -252,10 +254,10 @@ const Tm = {
   ${n ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${n}</p>` : ""}
   ${i ? `<h5>Evidence</h5><ul class="no-bullet">${i.map((s) => {
     const u = s === "Glue project" ? "PXD012174" : s;
-    return `<li title='${u}' style="padding: .25rem 0">${u}&nbsp;
-              (<a href="https://proteomecentral.proteomexchange.org/dataset/${u}" style="color:#FFF" target="_blank">ProteomeXchange</a>)
+    return `<li title='${u}'>${u}&nbsp;
+              (<a href="https://proteomecentral.proteomexchange.org/dataset/${u}" target="_blank">ProteomeXchange</a>)
               </li>
-              ${s === "Glue project" ? '<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>' : ""}
+              ${s === "Glue project" ? '<li title="publication">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" target="_blank">PubMed</a>)</li>' : ""}
               `;
   }).join("")}</ul>` : ""}`;
 }, EBe = {
@@ -268,16 +270,16 @@ const Tm = {
   185431: { build: "590", organism: "T Brucei" }
 }, MBe = (e) => {
   if (e.name?.toLowerCase() === "PubMed".toLowerCase())
-    return `${e.id}&nbsp;(<a href='${e.url}' style="color:#FFF" target='_blank'>${e.name}</a>&nbsp;<a href='${e.alternativeUrl}' style="color:#FFF" target='_blank'>EuropePMC</a>)`;
-  const t = `&nbsp;<a href='${e.url}' style="color:#FFF" target='_blank'>${e.id}</a>`;
+    return `${e.id}&nbsp;(<a href='${e.url}' target='_blank'>${e.name}</a>&nbsp;<a href='${e.alternativeUrl}' target='_blank'>EuropePMC</a>)`;
+  const t = `&nbsp;<a href='${e.url}' target='_blank'>${e.id}</a>`;
   return e.name ? e.name.startsWith("Hpp") ? `${t}&nbsp;(${e.name.slice(3)})` : `${t}&nbsp;(${e.name})` : t;
 }, vAe = (e) => e ? `
         <ul class="no-bullet">${e.map((t) => {
   const r = TBe.find((n) => n.name === t.code);
-  return r ? `<li title='${r.description}' style="padding: .25rem 0">${r.shortDescription}:&nbsp;${t.source ? MBe(t.source) : ""}</li>` : "";
+  return r ? `<li title='${r.description}'>${r.shortDescription}:&nbsp;${t.source ? MBe(t.source) : ""}</li>` : "";
 }).join("")}</ul>
       ` : "", gAe = (e) => `<ul class="no-bullet">${e.map(
-  (t) => `<li style="padding: .25rem 0">${t.name} ${t.url ? `<a href="${t.url}" style="color:#FFF" target="_blank">${t.id}</a>` : `${t.name} ${t.id}`}</li>`
+  (t) => `<li>${t.name} ${t.url ? `<a href="${t.url}" target="_blank">${t.id}</a>` : `${t.name} ${t.id}`}</li>`
 ).join("")}</ul>`, $Be = (e, t) => {
   if (!e) return "";
   const r = e.flatMap(
@@ -286,7 +288,7 @@ const Tm = {
   return `
     <ul class="no-bullet">${n.map((a) => {
     const o = a === "Glue project" ? "PXD012174" : a;
-    return `<li title='${o}' style="padding: .25rem 0">${o}&nbsp;(<a href="${i}${o}" style="color:#FFF" target="_blank">ProteomeXchange</a>${a === "Glue project" ? ')</li><li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>' : `&nbsp;<a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=${EBe[t].build}" style="color:#FFF" target="_blank">PeptideAtlas</a>)</li>`}`;
+    return `<li title='${o}'>${o}&nbsp;(<a href="${i}${o}" target="_blank">ProteomeXchange</a>${a === "Glue project" ? ')</li><li title="publication">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" target="_blank">PubMed</a>)</li>' : `&nbsp;<a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=${EBe[t].build}" target="_blank">PeptideAtlas</a>)</li>`}`;
   }).join("")}</ul>
   `;
 }, kBe = (e, t) => {
@@ -306,7 +308,9 @@ const Tm = {
   const { peptide: r, begin: n } = e, i = Number(n) + t.position - 1, a = r.charAt(t.position - 1);
   return t.name === "Phosphorylation" ? `${i} ${pAe(a)}` : t.name === "SUMOylation" ? `${i} ${mAe(a)}` : "";
 }, yAe = (e, t) => {
-  const r = e.type === "PROTEOMICS_PTM" ? $Be(e.residuesToHighlight, t) : vAe(e.evidences), n = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.map((o) => Ene(e, o)), i = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.flatMap(
+  const r = e.type === "PROTEOMICS_PTM" ? $Be(e.residuesToHighlight, t) : vAe(e.evidences), n = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.map(
+    (o) => Ene(e, o)
+  ), i = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.flatMap(
     ({ dbReferences: o }) => o.map((s) => s.id)
   );
   let { description: a } = e;
@@ -330,20 +334,20 @@ const Tm = {
         ${e.unique ? `<h5>Unique</h5><p>${e.unique ? "Yes" : "No"}</p>` : ""}
         ${e.xrefs ? `<h5>Cross-references</h5>${gAe(e.xrefs)}` : ""}
         ${r ? `<h5>Evidence</h5>${r}` : ""}
-        ${e.residuesToHighlight && i && !i.includes("Glue project") ? `<hr /><h5 data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">PTM statistical attributes</h5><ul class="no-bullet">${e.residuesToHighlight.map(
+        ${e.residuesToHighlight && i && !i.includes("Glue project") ? `<hr /><h5 class="margin-bottom" data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">PTM statistical attributes</h5><ul class="no-bullet">${e.residuesToHighlight.map(
       (o) => o.dbReferences.map(
         (s) => `<li><b>${s.id}</b></li>
-                        <li style="text-indent: 1em"><b>${Ene(
+                        <li class="text-indent-1"><b>${Ene(
           e,
           o
         )}</b></li>
-                        ${s.properties["Pubmed ID"] ? `<li style="text-indent: 2em">PubMed ID: <a href="https://europepmc.org/article/MED/${s.properties["Pubmed ID"]}" style="color:#FFF" target="_blank">${s.properties["Pubmed ID"]}</a></li>` : ""}
-                        ${s.properties["Confidence score"] ? `<li style="text-indent: 2em"><span data-article-id="mod_res_large_scale#confidence-score">Confidence score</span>: ${s.properties["Confidence score"]}</li>` : ""}
-                        ${s.properties["Sumo isoforms"] ? `<li style="text-indent: 2em">SUMO family member: ${s.properties["Sumo isoforms"]}</li>` : ""}
-                        ${s.properties["Organism part"] ? `<li style="text-indent: 2em">Organism part: ${s.properties["Organism part"]}</li>` : ""}
-                        ${s.properties["PSM Count (0.05 gFLR)"] ? `<li style="text-indent: 2em">PSM Count (0.05 gFLR): ${s.properties["PSM Count (0.05 gFLR)"]}</li>` : ""}
-                        ${s.properties["Final site probability"] ? `<li style="text-indent: 2em">Final site probability: ${s.properties["Final site probability"]}</li>` : ""}
-                        ${s.properties["Universal Spectrum Id"] ? `<li style="text-indent: 2em; white-space: nowrap;">Universal Spectrum Id: 
+                        ${s.properties["Pubmed ID"] ? `<li class="text-indent-2">PubMed ID: <a href="https://europepmc.org/article/MED/${s.properties["Pubmed ID"]}" target="_blank">${s.properties["Pubmed ID"]}</a></li>` : ""}
+                        ${s.properties["Confidence score"] ? `<li class="text-indent-2"><span data-article-id="mod_res_large_scale#confidence-score">Confidence score</span>: ${s.properties["Confidence score"]}</li>` : ""}
+                        ${s.properties["Sumo isoforms"] ? `<li class="text-indent-2">SUMO family member: ${s.properties["Sumo isoforms"]}</li>` : ""}
+                        ${s.properties["Organism part"] ? `<li class="text-indent-2">Organism part: ${s.properties["Organism part"]}</li>` : ""}
+                        ${s.properties["PSM Count (0.05 gFLR)"] ? `<li class="text-indent-2">PSM Count (0.05 gFLR): ${s.properties["PSM Count (0.05 gFLR)"]}</li>` : ""}
+                        ${s.properties["Final site probability"] ? `<li class="text-indent-2">Final site probability: ${s.properties["Final site probability"]}</li>` : ""}
+                        ${s.properties["Universal Spectrum Id"] ? `<li class="text-indent-2 nowrap">Universal Spectrum Id: 
                         <a href="http://proteomecentral.proteomexchange.org/usi/?usi=${s.properties["Universal Spectrum Id"]}" target="_blank">View on ProteomeXchange</a>
                         </li>` : ""}                        
                         `
@@ -355,7 +359,7 @@ const Tm = {
   }
 }, IBe = (e) => `<ul>
               ${e.map(
-  (t) => `<li style="margin: 0.25rem 0"><a style="color:#FFF" href='${t.source.url}' target='_blank'>
+  (t) => `<li><a href='${t.source.url}' target='_blank'>
               ${t.source.id}
           </a> (${t.start}-${t.end})</li>`
 ).join("")}
@@ -60207,10 +60211,21 @@ let cm = class extends p2(m2(vv)) {
           font-weight: bold;
         }
 
+        .structure-viewer-message-content {
+          white-space: pre-wrap;
+          line-height: normal;
+        }
+
         .structure-viewer-messages > button {
-          font-size: 50%;
+          font-size: 75%;
           font-weight: bold;
-          margin-inline-start: 1ch;
+          position: absolute;
+          top: -2px;
+          right: 0px;
+          border: none;
+          background: transparent;
+          cursor: pointer;
+          padding: 0px 3px;
         }
       </style>
       <div id="molstar-parent" class="structure-viewer-container">
@@ -60219,7 +60234,11 @@ let cm = class extends p2(m2(vv)) {
           style="position: absolute; top: 0; left: 0; right: 0; bottom: 0"
         ></canvas>
         ${this.message ? uae`<div class="structure-viewer-messages">
-              <span>${(e = this.message) === null || e === void 0 ? void 0 : e.title}:</span> ${(t = this.message) === null || t === void 0 ? void 0 : t.content}
+              <span>${(e = this.message) === null || e === void 0 ? void 0 : e.title}</span>:
+              <span
+                class="structure-viewer-message-content"
+                .innerHTML=${(t = this.message) === null || t === void 0 ? void 0 : t.content}
+              ></span>
               <button
                 type="button"
                 title="close message"
@@ -60297,23 +60316,28 @@ let cm = class extends p2(m2(vv)) {
     this.message = null;
   }
   updateHighlight(e) {
-    if (!e?.length || e.some((i) => !Number.isInteger(i.position))) return;
+    if (!e?.length || e.some((a) => !Number.isInteger(a.position))) return;
     let t;
-    if (this.isAF()) t = e.map((i) => ({ start: i.position, end: i.position, entity: 1, chain: i.chain }));
+    if (this.isAF()) t = e.map((a) => ({ start: a.position, end: a.position, entity: 1, chain: a.chain }));
     else try {
-      t = e.flatMap((i) => {
-        var a;
-        return Jpe(i.position, i.position, "PDB_UP", (a = this.selectedMolecule) === null || a === void 0 ? void 0 : a.mappings).filter((o) => o.chain === i.chain);
+      t = e.flatMap((a) => {
+        var o;
+        return Jpe(a.position, a.position, "PDB_UP", (o = this.selectedMolecule) === null || o === void 0 ? void 0 : o.mappings).filter((s) => s.chain === a.chain);
       }).filter(Boolean);
-    } catch (i) {
-      if (i instanceof ME) return void this.showMessage("Error", i.message);
-      throw i;
+    } catch (a) {
+      if (a instanceof ME) return void this.showMessage("Error", a.message);
+      throw a;
     }
     if (!t.length) return void this.showMessage("Error", "Residue outside of sequence range");
-    const r = t.map((i) => `${i.start}:${i.end}`).join(",");
+    const r = t.map((a) => `${a.start}:${a.end}`).join(",");
     this.highlight = r;
-    const n = new CustomEvent("change", { detail: { highlight: r }, bubbles: !0, cancelable: !0 });
-    this.dispatchEvent(n);
+    const n = t.map((a, o) => {
+      const s = e[o].position, u = a.start === a.end ? a.start : `${a.start}:${a.end}`;
+      return `<span data-article-id="structure_section#description-of-structure-table-contents">Chain</span>: ${a.chain}, <span data-article-id="structure_section#description-of-structure-table-contents">Position</span>: ${s} <br /><b>${this["protein-accession"]}</b>: ${u}`;
+    }).join("");
+    this.showMessage(`${this["structure-id"]}`, n);
+    const i = new CustomEvent("change", { detail: { highlight: r }, bubbles: !0, cancelable: !0 });
+    this.dispatchEvent(i);
   }
   highlightChain() {
     var e, t, r, n;
@@ -60328,7 +60352,7 @@ let cm = class extends p2(m2(vv)) {
       if (a instanceof ME) return (t = ec(this, Es, "f")) === null || t === void 0 || t.clearHighlight(), void this.showMessage("Error", a.message);
       throw a;
     }
-    i?.length ? ((n = ec(this, Es, "f")) === null || n === void 0 || n.highlight(i), this.clearMessage()) : (r = ec(this, Es, "f")) === null || r === void 0 || r.clearHighlight();
+    i?.length ? (n = ec(this, Es, "f")) === null || n === void 0 || n.highlight(i) : (r = ec(this, Es, "f")) === null || r === void 0 || r.clearHighlight();
   }
 };
 Es = /* @__PURE__ */ new WeakMap(), J0([ZT({ type: String })], cm.prototype, "protein-accession", void 0), J0([ZT({ type: String })], cm.prototype, "structure-id", void 0), J0([ZT({ type: String })], cm.prototype, "custom-download-url", void 0), J0([ZT({ type: String })], cm.prototype, "color-theme", void 0), J0([lae()], cm.prototype, "selectedMolecule", void 0), J0([lae()], cm.prototype, "message", void 0), cm = J0([e$("nightingale-structure")], cm);