protvista-uniprot 4.2.0 → 4.2.1

package/README.md

@@ -87,3 +87,9 @@ detail: {
     hasData: true
 }
 ```
+
+## Publishing
+
+```
+npm login; rm -rf node_modules dist; yarn; yarn build; yarn publish; git push
+```

package/dist/protvista-uniprot.mjs

@@ -234,27 +234,28 @@ const km = {
 }, GEe = (e) => {
   const t = e.toUpperCase();
   return t in ise ? ise[t] : (console.error(`${t} not a valid amino acid for SUMOylation`), "");
-}, gHe = (e, t, n) => {
-  const r = [
-    ...e.flatMap(
-      ({ dbReferences: o }) => o?.flatMap(({ id: s }) => [s])
+}, gHe = (e, t, n, r) => {
+  const i = [
+    ...t.flatMap(
+      ({ dbReferences: s }) => s?.flatMap(({ id: u }) => [u])
     )
   ];
-  let i;
-  const a = new Set(e.flatMap(({ name: o }) => o));
-  return a.size && (a.size > 1 ? console.error(
+  let a;
+  const o = new Set(t.flatMap(({ name: s }) => s));
+  return o.size && (o.size > 1 ? console.error(
     `PTMeXchange PTM has a mixture of modifications: ${Array.from(
-      a
+      o
     )}`
-  ) : [i] = a), `
-  <h5>Description</h5><p>${i === "Phosphorylation" ? HEe(t) : GEe(t)}</p>
-  ${n ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${n}</p>` : ""}
-  ${`<h5>Evidence</h5><ul class="no-bullet">${r.map((o) => {
-    const s = o === "Glue project" ? "PXD012174" : o;
-    return `<li title='${s}' style="padding: .25rem 0">${s}&nbsp;
-              (<a href="https://proteomecentral.proteomexchange.org/dataset/${s}" style="color:#FFF" target="_blank">ProteomeXchange</a>)
+  ) : [a] = o), `
+  ${e ? `<h4>${e}</h4><hr />` : ""}
+  <h5>Description</h5><p>${a === "Phosphorylation" ? HEe(n) : GEe(n)}</p>
+  ${r ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${r}</p>` : ""}
+  ${`<h5>Evidence</h5><ul class="no-bullet">${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>)
               </li>
-              ${o === "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" 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>' : ""}
               `;
   }).join("")}</ul>`}`;
 }, yHe = {
@@ -97608,7 +97609,10 @@ const JFt = (e) => {
         a,
         UEe(a, e.taxid)
       );
-    }, []) : t = e.features.map((r) => Object.assign(r, UEe(r, e.taxid))), t = M7e(t);
+    }, []) : t = e.features.map((r) => Object.assign(
+      r,
+      UEe(r, e.taxid)
+    )), t = M7e(t);
   }
   return t;
 }, tLt = "PDBE_COVER", nLt = "STRUCTURE_COVERAGE", rLt = (e) => e.charAt(0).toUpperCase() + e.slice(1), iLt = (e) => Object.keys(e).reduce(
@@ -97949,58 +97953,62 @@ class yLt {
     return mLt(n);
   }
 }
-const vLt = new yLt({
-  hash: "bkdr",
-  saturation: [0.65, 0.35, 0.5],
-  lightness: [0.65, 0.35, 0.5]
-}), bLt = (e) => {
-  try {
-    return e?.results?.map(({ metadata: t, proteins: n }) => ({
-      ...t,
-      locations: n[0].entry_protein_locations,
-      start: n[0].entry_protein_locations ? Math.min(
-        ...n[0].entry_protein_locations.map(
-          (r) => Math.min(...r.fragments.map((i) => i.start))
-        )
-      ) : "",
-      end: n[0].entry_protein_locations ? Math.max(
-        ...n[0].entry_protein_locations?.map(
-          (r) => Math.max(...r.fragments.map((i) => i.end))
-        )
-      ) : "",
-      color: vLt.hex(
-        t.accession.toLowerCase().split("").reverse().join("")
-      ),
-      tooltipContent: `
+const vLt = (e, t, n) => `
+      ${e && t ? `<h4>InterPro Representative Domain ${e}-${t}</h4><hr />` : ""}
         <h5>Accession</h5>
         <p>
         <a
           target="_blank"
           rel="noopener"
-          href="https://www.ebi.ac.uk/interpro/entry/${t.source_database}/${t.accession}/"
+          href="https://www.ebi.ac.uk/interpro/entry/${n.source_database}/${n.accession}/"
         >
-        ${t.accession}
+        ${n.accession}
         </a>
         </p>
         <h5>Name</h5>
-        <p>${t.name}</p>
-        ${t.integrated ? `<h5>Integrated into </h5>
+        <p>${n.name}</p>
+        ${n.integrated ? `<h5>Integrated into </h5>
         <p>
         <a
           target="_blank"
           rel="noopener"
-          href="https://www.ebi.ac.uk/interpro/entry/InterPro/${t.integrated}/"
+          href="https://www.ebi.ac.uk/interpro/entry/InterPro/${n.integrated}/"
         >
-          ${t.integrated}
+          ${n.integrated}
         </a>
         </p>` : ""}
-      `,
-      length: n[0].protein_length
-    }));
+      `, bLt = new yLt({
+  hash: "bkdr",
+  saturation: [0.65, 0.35, 0.5],
+  lightness: [0.65, 0.35, 0.5]
+}), _Lt = (e) => {
+  try {
+    return e?.results?.map(({ metadata: t, proteins: n }) => {
+      const r = n[0].entry_protein_locations ? Math.min(
+        ...n[0].entry_protein_locations.map(
+          (a) => Math.min(...a.fragments.map((o) => o.start))
+        )
+      ) : "", i = n[0].entry_protein_locations ? Math.max(
+        ...n[0].entry_protein_locations?.map(
+          (a) => Math.max(...a.fragments.map((o) => o.end))
+        )
+      ) : "";
+      return {
+        ...t,
+        locations: n[0].entry_protein_locations,
+        start: r,
+        end: i,
+        color: bLt.hex(
+          t.accession.toLowerCase().split("").reverse().join("")
+        ),
+        tooltipContent: vLt(r, i, t),
+        length: n[0].protein_length
+      };
+    });
   } catch {
     throw new Error("Failed transforming the data");
   }
-}, _Lt = (e) => {
+}, xLt = (e) => {
   if (e.sequence && e.features.length) {
     const t = e.features.map((o) => ({
       ...o,
@@ -98036,7 +98044,7 @@ const vLt = new yLt({
       }
     ];
   }
-}, xLt = (e) => {
+}, wLt = (e) => {
   if (e.sequence && e.features.length) {
     const t = new Uint8ClampedArray(e.sequence.length), n = new Uint8ClampedArray(e.sequence.length), r = new Uint8ClampedArray(e.sequence.length);
     for (const o of e.features) {
@@ -98065,19 +98073,19 @@ const vLt = new yLt({
       // },
     ];
   }
-}, wLt = (e) => e.dbReferenceType.find((t) => t.type === "rna_editing")?.id, SLt = (e) => `http://srv00.recas.ba.infn.it/cgi/atlas/getpage_dev.py?query9=hg&query10=hg38&acc=${e}`, ALt = (e) => `https://www.ensembl.org/id/${e}`, CLt = (e) => {
-  const t = [], n = wLt(e);
+}, SLt = (e) => e.dbReferenceType.find((t) => t.type === "rna_editing")?.id, ALt = (e) => `http://srv00.recas.ba.infn.it/cgi/atlas/getpage_dev.py?query9=hg&query10=hg38&acc=${e}`, CLt = (e) => `https://www.ensembl.org/id/${e}`, $Lt = (e) => {
+  const t = [], n = SLt(e);
   n && t.push(
-    `REDIportal <a href="${SLt(
+    `REDIportal <a href="${ALt(
       n
     )}" target="_blank">${n}</a>`
   );
   for (const r of e.variantType.variantLocation)
     r.source === "Ensembl" && t.push(
-      `Ensembl <a href="${ALt(r.seqId)}" target="_blank">${r.seqId}</a>`
+      `Ensembl <a href="${CLt(r.seqId)}" target="_blank">${r.seqId}</a>`
     );
   return t.length === 0 ? "" : `<br><ul class="no-bullet">${t.map((r) => `<li>${r}</li>`).join("")}</ul>`;
-}, $Lt = (e) => `
+}, ELt = (e) => `
   ${e.start && e.end ? `<h4>RNA Edit ${e.start}-${e.end}</h4><hr />` : ""}
   <h5>Variant</h5>
   <p>${e.variantType.wildType} > ${e.variantType.mutatedType}</p>
@@ -98085,8 +98093,8 @@ const vLt = new yLt({
   <p>${e.consequenceType}</p>
   <h5>Location</h5>
   <ul class="no-bullet">${e.variantType.genomicLocation.map((t) => `<li>${t}</li>`).join("")}
-  ${CLt(e)}
-  `, ELt = ({
+  ${$Lt(e)}
+  `, TLt = ({
   sequence: e,
   features: t = []
 }) => ({
@@ -98102,11 +98110,11 @@ const vLt = new yLt({
       tooltipContent: ""
       // Set with transformed feature below,
     };
-    return r.tooltipContent = $Lt(r), r;
+    return r.tooltipContent = ELt(r), r;
   })
 });
 var gze = /* @__PURE__ */ ((e) => (e.Gold = "#c39b00", e.Silver = "#8194a1", e.Bronze = "#a65708", e))(gze || {});
-const TLt = (e, t, n) => {
+const PLt = (e, t, n) => {
   const r = new Set(
     e.flatMap(
       ({ dbReferences: a }) => a?.map(({ properties: o }) => o["Confidence score"])
@@ -98121,10 +98129,15 @@ const TLt = (e, t, n) => {
     start: n,
     end: n,
     shape: "triangle",
-    tooltipContent: gHe(e, t, i),
+    tooltipContent: gHe(
+      `MOD_RES_LS ${n}-${n}`,
+      e,
+      t,
+      i
+    ),
     color: i && gze[i] || "black"
   };
-}, PLt = (e) => {
+}, MLt = (e) => {
   if (e) {
     const { features: t } = e, n = {};
     if (t) {
@@ -98143,25 +98156,25 @@ const TLt = (e, t, n) => {
           ) : n[a].ptms.push(i) : n[a] = { ptms: [i], aa: o };
         }
       return Object.entries(n).map(
-        ([r, { ptms: i, aa: a }]) => TLt(i, a, +r)
+        ([r, { ptms: i, aa: a }]) => PLt(i, a, +r)
       );
     }
   }
   return [];
-}, MLt = (e) => {
+}, kLt = (e) => {
   const t = e?.[0]?.cifUrl;
   return t?.length ? t.replace("-model", "-confidence").replace(".cif", ".json") : null;
-}, kLt = async (e) => {
+}, ILt = async (e) => {
   try {
     return (await fetch(e)).json();
   } catch (t) {
     console.error("Could not load AlphaFold confidence", t);
   }
-}, ILt = async (e, t) => {
-  const n = MLt(e), { uniprotSequence: r } = e?.[0] || {};
+}, OLt = async (e, t) => {
+  const n = kLt(e), { uniprotSequence: r } = e?.[0] || {};
   if (n && r === t.sequence.sequence)
-    return (await kLt(n))?.confidenceCategory.join("");
-}, OLt = 0.34, DLt = 0.564, yze = /\s*\n\s*/, vze = /^(.)(\d+)(.),(.+),(\w+)$/, NLt = (e) => {
+    return (await ILt(n))?.confidenceCategory.join("");
+}, DLt = 0.34, NLt = 0.564, yze = /\s*\n\s*/, vze = /^(.)(\d+)(.),(.+),(\w+)$/, RLt = (e) => {
   const t = [];
   for (const [r, i] of e.split(yze).entries()) {
     if (r === 0 || !i)
@@ -98189,21 +98202,21 @@ const TLt = (e, t, n) => {
       (o, s) => o + +s.pathogenicityScore,
       0
     ) / r.length;
-    a > DLt ? i = "P" : a < OLt && (i = "B"), n.push(i);
+    a > NLt ? i = "P" : a < DLt && (i = "B"), n.push(i);
   }
   return n.join("");
-}, RLt = async (e) => {
+}, BLt = async (e) => {
   try {
     const n = await (await fetch(e)).text();
-    return NLt(n);
+    return RLt(n);
   } catch (t) {
     console.error("Could not load AlphaMissense pathogenicity", t);
   }
-}, BLt = async (e, t) => {
+}, FLt = async (e, t) => {
   const { amAnnotationsUrl: n, uniprotSequence: r } = e?.[0] || {};
   if (n && r === t.sequence.sequence)
-    return await RLt(n);
-}, FLt = (e) => {
+    return await BLt(n);
+}, LLt = (e) => {
   const t = [];
   for (const [n, r] of e.split(yze).entries()) {
     if (n === 0 || !r)
@@ -98216,18 +98229,18 @@ const TLt = (e, t, n) => {
     });
   }
   return t;
-}, LLt = async (e) => {
+}, ULt = async (e) => {
   try {
     const n = await (await fetch(e)).text();
-    return FLt(n);
+    return LLt(n);
   } catch (t) {
     console.error("Could not load AlphaMissense pathogenicity", t);
   }
-}, ULt = async (e, t) => {
+}, zLt = async (e, t) => {
   const { amAnnotationsUrl: n, uniprotSequence: r } = e?.[0] || {};
   if (n && r === t.sequence.sequence)
-    return await LLt(n);
-}, Ld = "https://www.ebi.ac.uk/proteins/api/", zEe = "https://alphafold.ebi.ac.uk/api/", zLt = "https://alphafold.ebi.ac.uk/entry/", jLt = "https://www.ebi.ac.uk/interpro/api/", Xn = {
+    return await ULt(n);
+}, Ld = "https://www.ebi.ac.uk/proteins/api/", zEe = "https://alphafold.ebi.ac.uk/api/", jLt = "https://alphafold.ebi.ac.uk/entry/", HLt = "https://www.ebi.ac.uk/interpro/api/", Xn = {
   proteins: `${Ld}proteins/`,
   features: `${Ld}features/`,
   variation: `${Ld}variation/`,
@@ -98237,7 +98250,7 @@ const TLt = (e, t, n) => {
   nonPtm: `${Ld}proteomics/nonPtm/`,
   ptm: `${Ld}proteomics/ptm/`,
   hpp: `${Ld}proteomics/hpp/`
-}, HLt = {
+}, GLt = {
   categories: [
     {
       name: "MOLECULE_PROCESSING",
@@ -98480,7 +98493,7 @@ const TLt = (e, t, n) => {
           data: [
             {
               adapter: "interpro-adapter",
-              url: `${jLt}entry/all/protein/uniprot/{accession}?type=domain&page_size=100`
+              url: `${HLt}entry/all/protein/uniprot/{accession}?type=domain&page_size=100`
             }
           ],
           tooltip: "InterPro representative domains"
@@ -98939,7 +98952,7 @@ const TLt = (e, t, n) => {
         {
           name: "alphafold_confidence",
           label: "AlphaFold Confidence",
-          labelUrl: `${zLt}{accession}`,
+          labelUrl: `${jLt}{accession}`,
           trackType: "nightingale-colored-sequence",
           data: [
             {
@@ -99054,7 +99067,7 @@ const TLt = (e, t, n) => {
       ]
     }
   ]
-}, GLt = oee`
+}, VLt = oee`
   .track-content {
     width: 80vw;
   }
@@ -99141,24 +99154,24 @@ const TLt = (e, t, n) => {
     cursor: pointer;
   }
 `;
-var VLt = Object.defineProperty, qLt = Object.getOwnPropertyDescriptor, WLt = (e, t, n, r) => {
-  for (var i = r > 1 ? void 0 : r ? qLt(t, n) : t, a = e.length - 1, o; a >= 0; a--)
+var qLt = Object.defineProperty, WLt = Object.getOwnPropertyDescriptor, XLt = (e, t, n, r) => {
+  for (var i = r > 1 ? void 0 : r ? WLt(t, n) : t, a = e.length - 1, o; a >= 0; a--)
     (o = e[a]) && (i = (r ? o(t, n, i) : o(i)) || i);
-  return r && i && VLt(t, n, i), i;
+  return r && i && qLt(t, n, i), i;
 };
-const XLt = {
+const YLt = {
   "feature-adapter": JFt,
-  "interpro-adapter": bLt,
+  "interpro-adapter": _Lt,
   "proteomics-adapter": eLt,
   "structure-adapter": uLt,
   "variation-adapter": lLt,
-  "variation-graph-adapter": _Lt,
-  "rna-editing-adapter": ELt,
-  "rna-editing-graph-adapter": xLt,
-  "proteomics-ptm-adapter": PLt,
-  "alphafold-confidence-adapter": ILt,
-  "alphamissense-pathogenicity-adapter": BLt,
-  "alphamissense-heatmap-adapter": ULt
+  "variation-graph-adapter": xLt,
+  "rna-editing-adapter": TLt,
+  "rna-editing-graph-adapter": wLt,
+  "proteomics-ptm-adapter": MLt,
+  "alphafold-confidence-adapter": OLt,
+  "alphamissense-pathogenicity-adapter": FLt,
+  "alphamissense-heatmap-adapter": zLt
 };
 let jEe = class extends Vw {
   constructor() {
@@ -99178,7 +99191,7 @@ let jEe = class extends Vw {
   }
   addStyles() {
     const e = document.createElement("style");
-    e.innerHTML = `${GLt.toString()} ${O7e.toString()}`, document.querySelector("head")?.append(e);
+    e.innerHTML = `${VLt.toString()} ${O7e.toString()}`, document.querySelector("head")?.append(e);
   }
   registerWebComponents() {
     qc("nightingale-navigation", FSt), qc("nightingale-track", N9e), qc("nightingale-colored-sequence", GCt), qc("nightingale-interpro-track", CTt), qc("nightingale-sequence", WNe), qc("nightingale-variation", hMt), qc("nightingale-linegraph-track", XIt), qc("nightingale-filter", QFt), qc("nightingale-manager", Z2t), qc("protvista-uniprot-structure", O2t), qc("nightingale-sequence-heatmap", gBt);
@@ -99201,7 +99214,7 @@ let jEe = class extends Vw {
             );
             if (!d || l === "variation-adapter" && d[0].length === 0)
               return;
-            let f = l ? await XLt[l].apply(null, d) : d;
+            let f = l ? await YLt[l].apply(null, d) : d;
             if (l === "interpro-adapter") {
               const p = [];
               f?.forEach(
@@ -99289,7 +99302,7 @@ let jEe = class extends Vw {
     this._loadDataInComponents();
   }
   _init() {
-    this.config || (this.config = HLt), this.accession && (this.loadEntry(this.accession).then((e) => {
+    this.config || (this.config = GLt), this.accession && (this.loadEntry(this.accession).then((e) => {
       this.sequence = e.sequence.sequence, this.displayCoordinates = { start: 1, end: this.sequence?.length };
     }), this._loadData());
   }
@@ -99608,7 +99621,7 @@ let jEe = class extends Vw {
     }
   }
 };
-jEe = WLt([
+jEe = XLt([
   _Te("protvista-uniprot")
 ], jEe);
 export {