@jbrowse/core 3.6.4 → 3.7.0

package/BaseFeatureWidget/util.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stitch = stitch;
-exports.dedupe = dedupe;
+exports.filterSuccessiveElementsWithSameStartAndEndCoord = filterSuccessiveElementsWithSameStartAndEndCoord;
 exports.revlist = revlist;
 exports.calculateUTRs = calculateUTRs;
 exports.calculateUTRs2 = calculateUTRs2;
@@ -14,7 +14,7 @@ function stitch(subfeats, sequence) {
 function getItemId(feat) {
     return `${feat.start}-${feat.end}`;
 }
-function dedupe(list) {
+function filterSuccessiveElementsWithSameStartAndEndCoord(list) {
     return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
 }
 function revlist(list, seqlen) {
@@ -30,21 +30,37 @@ function calculateUTRs(cds, exons) {
     if (!cds.length) {
         return [];
     }
+    if (exons.length < cds.length) {
+        console.warn('exons.length less than cds.length, cant calculate UTR properly', { exons, cds });
+        return [];
+    }
     const firstCds = cds.at(0);
     const lastCds = cds.at(-1);
     const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
     const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
     const lastCdsExon = exons[lastCdsIdx];
     const firstCdsExon = exons[firstCdsIdx];
-    const fiveUTRs = [
+    const fivePrimeUTRs = [
         ...exons.slice(0, firstCdsIdx),
-        { start: firstCdsExon.start, end: firstCds.start },
-    ].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
-    const threeUTRs = [
-        { start: lastCds.end, end: lastCdsExon.end },
+        {
+            start: firstCdsExon.start,
+            end: firstCds.start,
+        },
+    ].map(elt => ({
+        ...elt,
+        type: 'five_prime_UTR',
+    }));
+    const threePrimeUTRs = [
+        {
+            start: lastCds.end,
+            end: lastCdsExon.end,
+        },
         ...exons.slice(lastCdsIdx + 1),
-    ].map(elt => ({ ...elt, type: 'three_prime_UTR' }));
-    return [...fiveUTRs, ...threeUTRs];
+    ].map(elt => ({
+        ...elt,
+        type: 'three_prime_UTR',
+    }));
+    return [...fivePrimeUTRs, ...threePrimeUTRs];
 }
 function calculateUTRs2(cds, parentFeat) {
     if (!cds.length) {
@@ -52,12 +68,25 @@ function calculateUTRs2(cds, parentFeat) {
     }
     const firstCds = cds.at(0);
     const lastCds = cds.at(-1);
-    const fiveUTRs = [{ start: parentFeat.start, end: firstCds.start }].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
-    const threeUTRs = [{ start: lastCds.end, end: parentFeat.end }].map(elt => ({
+    const fivePrimeUTRs = [
+        {
+            start: parentFeat.start,
+            end: firstCds.start,
+        },
+    ].map(elt => ({
+        ...elt,
+        type: 'five_prime_UTR',
+    }));
+    const threePrimeUTRs = [
+        {
+            start: lastCds.end,
+            end: parentFeat.end,
+        },
+    ].map(elt => ({
         ...elt,
         type: 'three_prime_UTR',
     }));
-    return [...fiveUTRs, ...threeUTRs];
+    return [...fivePrimeUTRs, ...threePrimeUTRs];
 }
 function ellipses(slug) {
     return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;

package/PluginLoader.js

@@ -78,7 +78,7 @@ function pluginUrl(d) {
     }
 }
 function isInWebWorker() {
-    return Boolean('WorkerGlobalScope' in globalThis);
+    return 'WorkerGlobalScope' in globalThis;
 }
 class PluginLoader {
     constructor(defs = [], args) {

package/assemblyManager/assembly.d.ts

@@ -45,6 +45,7 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
     readonly refNames: string[] | undefined;
 } & {
     getCanonicalRefName(refName: string): string | undefined;
+    getCanonicalRefName2(asmName: string): string;
     getRefNameColor(refName: string): string | undefined;
     isValidRefName(refName: string): boolean;
 } & {

package/assemblyManager/assembly.js

@@ -162,6 +162,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
             }
             return (self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]);
         },
+        getCanonicalRefName2(asmName) {
+            return this.getCanonicalRefName(asmName) || asmName;
+        },
         getRefNameColor(refName) {
             if (!self.refNames) {
                 return undefined;

package/assemblyManager/assemblyManager.d.ts

@@ -37,6 +37,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -105,6 +106,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -171,6 +173,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -208,6 +211,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
 } & {
     getCanonicalAssemblyName(asmName: string): string | undefined;
+    getCanonicalAssemblyName2(asmName: string): string;
     get(asmName: string): ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -240,6 +244,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -306,6 +311,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -377,6 +383,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -443,6 +450,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
+        getCanonicalRefName2(asmName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {

package/assemblyManager/assemblyManager.js

@@ -29,6 +29,10 @@ function assemblyManagerFactory(conf, pm) {
             var _a;
             return (_a = self.assemblyNameMap[asmName]) === null || _a === void 0 ? void 0 : _a.name;
         },
+        getCanonicalAssemblyName2(asmName) {
+            var _a;
+            return ((_a = self.assemblyNameMap[asmName]) === null || _a === void 0 ? void 0 : _a.name) || asmName;
+        },
         get(asmName) {
             if (asmName) {
                 const assembly = self.assemblyNameMap[asmName];

package/configuration/configurationSchema.js

@@ -33,8 +33,8 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
         options = {
             ...inputOptions.baseConfiguration.jbrowseSchemaOptions,
             ...inputOptions,
+            baseConfiguration: undefined,
         };
-        options.baseConfiguration = undefined;
     }
     return { schemaDefinition, options };
 }

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js

@@ -59,7 +59,7 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
         });
     }
     getRegionFeatureDensityStats(region, opts) {
-        let lastTime = +Date.now();
+        let lastTime = Date.now();
         const statsFromInterval = async (length, expansionTime) => {
             const { start, end } = region;
             const sampleCenter = start * 0.75 + end * 0.25;
@@ -83,7 +83,7 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
                 return stats;
             }
             else if (expansionTime <= 5000) {
-                const currTime = +Date.now();
+                const currTime = Date.now();
                 expansionTime += currTime - lastTime;
                 lastTime = currTime;
                 return statsFromInterval(interval * 2, expansionTime);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "3.6.4",
+  "version": "3.7.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -44,7 +44,7 @@
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.2.0",
+    "dompurify": "^3.3.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "generic-filehandle2": "^2.0.1",
@@ -54,7 +54,6 @@
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "rbush": "^3.0.1",
     "react-draggable": "^4.4.5",
     "rxjs": "^7.0.0",
     "serialize-error": "^8.0.0",
@@ -69,5 +68,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }