protvista-uniprot 4.3.7 → 4.4.0

package/src/protvista-uniprot.ts

@@ -16,7 +16,6 @@ import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequen
 import NightingaleFilter, {
   Filter,
 } from '@nightingale-elements/nightingale-filter';
-import { amColorScale } from '@nightingale-elements/nightingale-structure';
 
 // adapters
 import featureAdapter from './adapters/feature-adapter';
@@ -295,11 +294,6 @@ class ProtvistaUniprot extends LitElement {
                 ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)),
               ] as string[];
               heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData);
-              heatmapComponent.updateComplete.then(() => {
-                heatmapComponent.heatmapInstance.setColor((d) =>
-                  amColorScale(d.score)
-                );
-              });
             }
           }
         }

package/src/tooltips/feature-tooltip.ts

@@ -1,10 +1,5 @@
 import ecoMap from '../adapters/config/evidence';
-import {
-  acetylate,
-  phosphorylate,
-  sumoylate,
-  ubiquitinate,
-} from './ptm-tooltip';
+import { phosphorylate, sumoylate } from './ptm-tooltip';
 
 const taxIdToPeptideAtlasBuildData = {
   '36329': { build: '542', organism: 'Plasmodium' },
@@ -106,18 +101,12 @@ const findModifiedResidueName = (feature, ptm) => {
   const { peptide, begin: peptideStart } = feature;
   const proteinLocation = Number(peptideStart) + ptm.position - 1;
   const modifiedResidue = peptide.charAt(ptm.position - 1); // CharAt index starts from 0
-  switch (ptm.name) {
-    case 'Phosphorylation':
-      return `${proteinLocation} ${phosphorylate(modifiedResidue)}`;
-    case 'SUMOylation':
-      return `${proteinLocation} ${sumoylate(modifiedResidue)}`;
-    case 'Ubiquitinylation':
-      return `${proteinLocation} ${ubiquitinate(modifiedResidue)}`;
-    case 'Acetylation':
-      return `${proteinLocation} ${acetylate(modifiedResidue)}`;
-    default:
-      return '';
+  if (ptm.name === 'Phosphorylation') {
+    return `${proteinLocation} ${phosphorylate(modifiedResidue)}`;
+  } else if (ptm.name === 'SUMOylation') {
+    return `${proteinLocation} ${sumoylate(modifiedResidue)}`;
   }
+  return '';
 };
 
 const formatTooltip = (feature, taxId?: string) => {
@@ -245,7 +234,7 @@ const formatTooltip = (feature, taxId?: string) => {
                         }
                         ${
                           ref.properties['Universal Spectrum Id']
-                            ? `<li class="text-indent-2 nowrap margin-bottom">Universal Spectrum Id: 
+                            ? `<li class="text-indent-2 nowrap">Universal Spectrum Id: 
                         <a href="http://proteomecentral.proteomexchange.org/usi/?usi=${ref.properties['Universal Spectrum Id']}" target="_blank">View on ProteomeXchange</a>
                         </li>`
                             : ``

package/src/tooltips/ptm-tooltip.ts

@@ -1,10 +1,6 @@
 import { PTM } from '../adapters/ptm-exchange-adapter';
 
-type Modification =
-  | 'Phosphorylation'
-  | 'SUMOylation'
-  | 'Ubiquitinylation'
-  | 'Acetylation';
+type Modification = 'Phosphorylation' | 'SUMOylation';
 
 const aaToPhosphorylated = {
   R: 'Phosphoarginine',
@@ -19,31 +15,6 @@ const aaToSumoylated = {
   K: 'Sumoylated lysine',
 };
 
-const aaToUbiquitinated = {
-  K: 'Ubiquitinated lysine',
-  S: 'Ubiquitinated serine',
-  T: 'Ubiquitinated threonine',
-  C: 'Ubiquitinated cysteine',
-};
-
-const aaToAcetylated = {
-  S: 'Acetylserine',
-  A: 'Acetylalanine',
-  G: 'Acetylglycine',
-  T: 'Acetylthreonine',
-  V: 'Acetylvaline',
-  C: 'Acetylcysteine',
-  E: 'Acetylglutamin acid',
-  D: 'Acetylaspartic acid',
-  N: 'Acetylasparagine',
-  Q: 'Acetylglutamine',
-  L: 'Acetyllucine',
-  I: 'Acetlyisolucine',
-  W: 'Acetyltryptophan',
-  F: 'Acetylphenylalanine',
-  K: 'Acetyllysine',
-};
-
 export const phosphorylate = (aa: string) => {
   const AA = aa.toUpperCase();
   if (AA in aaToPhosphorylated) {
@@ -62,39 +33,6 @@ export const sumoylate = (aa: string) => {
   return '';
 };
 
-export const ubiquitinate = (aa: string) => {
-  const AA = aa.toUpperCase();
-  if (AA in aaToUbiquitinated) {
-    return aaToUbiquitinated[AA as keyof typeof aaToUbiquitinated];
-  }
-  console.error(`${AA} not a valid amino acid for Ubiquitinylation`);
-  return '';
-};
-
-export const acetylate = (aa: string) => {
-  const AA = aa.toUpperCase();
-  if (AA in aaToAcetylated) {
-    return aaToAcetylated[AA as keyof typeof aaToAcetylated];
-  }
-  console.error(`${AA} not a valid amino acid for Acetylation`);
-  return '';
-};
-
-const getDescription = (modification: Modification, aa: string) => {
-  switch (modification) {
-    case 'Phosphorylation':
-      return phosphorylate(aa);
-    case 'SUMOylation':
-      return sumoylate(aa);
-    case 'Ubiquitinylation':
-      return ubiquitinate(aa);
-    case 'Acetylation':
-      return acetylate(aa);
-    default:
-      return '';
-  }
-};
-
 const formatTooltip = (
   title: string,
   ptms: PTM[],
@@ -114,7 +52,7 @@ const formatTooltip = (
   if (modifications.size) {
     if (modifications.size > 1) {
       console.error(
-        `The ptms are grouped by modification, but more than one type detected: ${Array.from(
+        `PTMeXchange PTM has a mixture of modifications: ${Array.from(
           modifications
         )}`
       );
@@ -125,7 +63,9 @@ const formatTooltip = (
 
   return `
   ${title ? `<h4>${title}</h4><hr />` : ''}
-  <h5>Description</h5><p>${getDescription(modification, aa)}</p>
+  <h5>Description</h5><p>${
+    modification === 'Phosphorylation' ? phosphorylate(aa) : sumoylate(aa)
+  }</p>
   ${
     confidenceScore
       ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`