react-mutation-mapper 0.8.33 → 0.8.36

package/dist/component/track/ExonTrack.d.ts

@@ -11,6 +11,8 @@ export default class ExonTrack extends React.Component<ExonTrackProps, {}> {
     constructor(props: any);
     get transcriptId(): string | undefined;
     get transcript(): EnsemblTranscript | undefined;
+    get chromosome(): string;
+    get genomeBuild(): string;
     get exonSpecs(): TrackItemSpec[];
     get trackTitle(): JSX.Element;
     render(): JSX.Element;

package/dist/index.es.js

@@ -15,7 +15,7 @@ import { OncoKbAPI } from 'oncokb-ts-api-client';
 import Select, { components } from 'react-select';
 import $ from 'jquery';
 import Slider from 'react-rangeslider';
-import request from 'superagent';
+import request, { get } from 'superagent';
 import memoize from 'memoize-weak-decorator';
 import { cached } from 'mobxpromise';
 
@@ -8467,8 +8467,24 @@ var ExonTrack = /** @class */ (function (_super) {
         enumerable: false,
         configurable: true
     });
+    Object.defineProperty(ExonTrack.prototype, "chromosome", {
+        get: function () {
+            var _a, _b;
+            return (_b = (_a = this.props.store.ensemblTranscriptLookUp.result) === null || _a === void 0 ? void 0 : _a.body) === null || _b === void 0 ? void 0 : _b.seq_region_name;
+        },
+        enumerable: false,
+        configurable: true
+    });
+    Object.defineProperty(ExonTrack.prototype, "genomeBuild", {
+        get: function () {
+            return this.props.store.genomeBuild;
+        },
+        enumerable: false,
+        configurable: true
+    });
     Object.defineProperty(ExonTrack.prototype, "exonSpecs", {
         get: function () {
+            var _this = this;
             if (!this.transcriptId || !this.transcript) {
                 return [];
             }
@@ -8482,10 +8498,15 @@ var ExonTrack = /** @class */ (function (_super) {
                 ? exonInfo.map(function (exon, index) {
                     var startCodon = exon.start;
                     var endCodon = exon.start + exon.length;
-                    var exonLength = exon.length;
-                    var stringStart = formatExonLocation(startCodon, index);
-                    var stringEnd = formatExonLocation(endCodon);
-                    var stringLength = formatExonLength(exonLength);
+                    var exonStartLocation = formatExonLocation(startCodon, index);
+                    var exonEndLocation = formatExonLocation(endCodon);
+                    var exonLength = formatExonLength(exon.length);
+                    var link = _this.chromosome
+                        ? "https://igv.org/app/?locus=chr" + _this.chromosome + ":" + exon.genomicLocationStart + "-" + exon.genomicLocationEnd + "&genome=" + _this.genomeBuild
+                        : 'https://igv.org';
+                    var linkText = _this.chromosome
+                        ? _this.genomeBuild + ":chr" + _this.chromosome + ":" + exon.genomicLocationStart + " - " + exon.genomicLocationEnd
+                        : exon.genomicLocationStart + " - " + exon.genomicLocationEnd;
                     return {
                         color: altColors[index % 2],
                         startCodon: startCodon,
@@ -8497,14 +8518,41 @@ var ExonTrack = /** @class */ (function (_super) {
                                 " Exon ",
                                 exon.rank,
                                 " "),
-                            "Start: ",
-                            stringStart,
+                            "Start: Nucleotide",
+                            ' ',
+                            createElement("strong", null, exonStartLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            createElement("strong", null, exonStartLocation.aminoAcidLocation),
+                            createElement("br", null),
+                            "End: Nucleotide",
+                            ' ',
+                            createElement("strong", null, exonEndLocation.nucleotideLocation),
+                            ' ',
+                            "of amino acid",
+                            ' ',
+                            createElement("strong", null, exonEndLocation.aminoAcidLocation),
                             createElement("br", null),
-                            "End: ",
-                            stringEnd,
+                            "Length:",
+                            ' ',
+                            createElement("strong", null, exonLength.aminoAcidLength),
+                            ' ',
+                            "amino acids",
+                            ' ',
+                            exonLength.nucleotideLength && (createElement(Fragment, null,
+                                ' ',
+                                "and",
+                                ' ',
+                                createElement("strong", null, exonLength.nucleotideLength),
+                                ' ',
+                                "nucleotides")),
                             createElement("br", null),
-                            "Length: ",
-                            stringLength)),
+                            "Genomic location:", " ",
+                            createElement("a", { target: "_blank", href: link, rel: "noopener noreferrer" },
+                                createElement(Fragment, null,
+                                    linkText, " ",
+                                    createElement("i", { className: "fa fa-external-link" }))))),
                     };
                 })
                 : [];
@@ -8535,6 +8583,12 @@ var ExonTrack = /** @class */ (function (_super) {
     __decorate([
         computed
     ], ExonTrack.prototype, "transcript", null);
+    __decorate([
+        computed
+    ], ExonTrack.prototype, "chromosome", null);
+    __decorate([
+        computed
+    ], ExonTrack.prototype, "genomeBuild", null);
     __decorate([
         computed
     ], ExonTrack.prototype, "exonSpecs", null);
@@ -11724,6 +11778,28 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 },
             })
         });
+        Object.defineProperty(this, "ensemblTranscriptLookUp", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: remoteData({
+                await: function () { return [_this.activeTranscript]; },
+                invoke: function () { return __awaiter(_this, void 0, void 0, function () {
+                    var ensemblTranscriptLookUpLink;
+                    return __generator(this, function (_a) {
+                        ensemblTranscriptLookUpLink = this.genomeBuild === 'hg19'
+                            ? "https://grch37.rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json"
+                            : "https://rest.ensembl.org/lookup/id/" + this.activeTranscript.result + "?content-type=application/json";
+                        return [2 /*return*/, this.activeTranscript.result
+                                ? get(ensemblTranscriptLookUpLink)
+                                : undefined];
+                    });
+                }); },
+                onError: function () {
+                    // fail silently, leave the error handling responsibility to the data consumer
+                },
+            })
+        });
         makeObservable(this);
     }
     Object.defineProperty(DefaultMutationMapperStore.prototype, "selectedTranscript", {
@@ -12033,6 +12109,13 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 0);
         }
     });
+    Object.defineProperty(DefaultMutationMapperStore.prototype, "genomeBuild", {
+        get: function () {
+            return this.config.genomeBuild || 'hg19';
+        },
+        enumerable: false,
+        configurable: true
+    });
     __decorate([
         observable
     ], DefaultMutationMapperStore.prototype, "_selectedTranscript", void 0);
@@ -12103,6 +12186,9 @@ var DefaultMutationMapperStore = /** @class */ (function () {
     __decorate([
         autobind
     ], DefaultMutationMapperStore.prototype, "getDefaultEntrezGeneId", null);
+    __decorate([
+        computed
+    ], DefaultMutationMapperStore.prototype, "genomeBuild", null);
     return DefaultMutationMapperStore;
 }());