@jbrowse/core 2.11.1 → 2.12.0

package/BaseFeatureWidget/SequenceFeatureDetails/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
+exports.splitString = exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
 // note that these are currently put into the style section instead of being
 // defined in classes to aid copy and paste to an external document e.g. word
 exports.intronColor = undefined;
@@ -9,3 +9,45 @@ exports.proteinColor = 'rgb(220,160,220)';
 exports.cdsColor = 'rgb(220,220,180)';
 exports.updownstreamColor = 'rgba(250,200,200)';
 exports.genomeColor = 'rgb(200,280,200)';
+function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0, splitSize = 10, }) {
+    var _a;
+    const numChunks = Math.ceil(str.length / charactersPerRow);
+    const chunks = new Array(numChunks);
+    let splitStart = currRemainder % 10;
+    let iter = 0;
+    let offset = 0;
+    for (; iter < numChunks + 1; ++iter) {
+        const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow;
+        const r = str.slice(offset, offset + inc);
+        if (!r) {
+            break;
+        }
+        if (showCoordinates) {
+            let res = '';
+            for (let i = 0, j = splitStart; i < r.length; i++, j++) {
+                // note: this adds a space at the start but it causes trouble to try to
+                // say e.g. j%splitSize==0 && j to try to only add non-zero spaces
+                if (j % splitSize === 0) {
+                    res += ' ';
+                    j = 0;
+                }
+                res += r[i];
+            }
+            if (res) {
+                chunks[iter] = res;
+            }
+        }
+        else {
+            chunks[iter] = r;
+        }
+        splitStart = 0; // after newline, reset
+        offset += inc;
+    }
+    return {
+        segments: chunks,
+        remainder: ((((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
+            (iter < 2 ? currRemainder : 0)) %
+            charactersPerRow,
+    };
+}
+exports.splitString = splitString;

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -52,13 +52,28 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("../util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("../util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
+        setIntronBp(f: number): void; /**
+         * #property
+         */
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -132,13 +147,28 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
         upperCaseCDS: boolean;
+        charactersPerRow: number;
+        feature: import("../util").SimpleFeatureSerialized | undefined;
+        mode: string;
     } & {
+        setFeature(f: import("../util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
-        setIntronBp(f: number): void;
+        setIntronBp(f: number): void; /**
+         * #property
+         */
         setUpperCaseCDS(f: boolean): void;
+        setShowCoordinates(f: "none" | "relative" | "genomic"): void;
+        setMode(mode: string): void;
+    } & {
+        readonly showCoordinates: boolean;
+        readonly showGenomicCoordsOption: boolean;
+        readonly hasCDS: boolean | undefined;
+        readonly hasExon: boolean | undefined;
+        readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/PluginManager.d.ts

@@ -151,16 +151,7 @@ export default class PluginManager {
         '@jbrowse/core/util/tracks': typeof import("./util/tracks");
         '@jbrowse/core/util/Base1DViewModel': import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-                refName: import("mobx-state-tree").ISimpleType<string>;
-                start: import("mobx-state-tree").ISimpleType<number>;
-                end: import("mobx-state-tree").ISimpleType<number>;
-                reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-            } & {
-                assemblyName: import("mobx-state-tree").ISimpleType<string>;
-            }, {
-                setRefName(newRefName: string): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("./util").Region[], import("./util").Region[], import("./util").Region[]>, [undefined]>;
             bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
             offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
             interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -193,7 +184,7 @@ export default class PluginManager {
                 offset: number;
                 start: number;
                 end: number;
-                reversed: boolean;
+                reversed?: boolean | undefined;
             };
             bpToPx({ refName, coord, regionNumber, }: {
                 refName: string;

package/ReExports/modules.d.ts

@@ -59,16 +59,7 @@ declare const libs: {
     '@jbrowse/core/util/tracks': typeof trackUtils;
     '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
         id: mst.IOptionalIType<mst.ISimpleType<string>, [undefined]>;
-        displayedRegions: mst.IArrayType<mst.IModelType<{
-            refName: mst.ISimpleType<string>;
-            start: mst.ISimpleType<number>;
-            end: mst.ISimpleType<number>;
-            reversed: mst.IOptionalIType<mst.ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: mst.ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, mst._NotCustomized, mst._NotCustomized>>;
+        displayedRegions: mst.IOptionalIType<mst.IType<coreUtil.Region[], coreUtil.Region[], coreUtil.Region[]>, [undefined]>;
         bpPerPx: mst.IType<number | undefined, number, number>;
         offsetPx: mst.IType<number | undefined, number, number>;
         interRegionPaddingWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
@@ -101,7 +92,7 @@ declare const libs: {
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         };
         bpToPx({ refName, coord, regionNumber, }: {
             refName: string;

package/configuration/util.js

@@ -41,17 +41,10 @@ function readConfObject(confObject, slotPath, args = {}) {
             //   })`,
             // )
         }
-        if (slot.expr) {
-            const appliedFunc = slot.expr.evalSync(args);
-            if ((0, mobx_state_tree_1.isStateTreeNode)(appliedFunc)) {
-                return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(appliedFunc)));
-            }
-            return appliedFunc;
-        }
-        if ((0, mobx_state_tree_1.isStateTreeNode)(slot)) {
-            return JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(slot)));
-        }
-        return slot;
+        const val = slot.expr ? slot.expr.evalSync(args) : slot;
+        return (0, mobx_state_tree_1.isStateTreeNode)(val)
+            ? JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(val)))
+            : val;
     }
     if (Array.isArray(slotPath)) {
         const slotName = slotPath[0];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -21,6 +21,8 @@
   "main": "index.js",
   "scripts": {
     "test": "cd ../..; jest packages/core",
+    "storybook": "storybook dev --port 6006",
+    "storybook:build": "storybook build",
     "coverage": "yarn test --coverage",
     "clean": "rimraf dist tsconfig.build.tsbuildinfo",
     "prebuild": "yarn clean",
@@ -31,6 +33,7 @@
     "@babel/runtime": "^7.17.9",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@mui/icons-material": "^5.0.1",
+    "@mui/x-data-grid": "^7.0.0",
     "@types/clone": "^2.0.0",
     "abortable-promise-cache": "^1.5.0",
     "canvas-sequencer": "^3.1.0",
@@ -58,7 +61,6 @@
   },
   "peerDependencies": {
     "@mui/material": "^5.0.0",
-    "@mui/x-data-grid": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -72,5 +74,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }

package/pluggableElementTypes/models/BaseDisplayModel.d.ts

@@ -121,9 +121,9 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
      * #method
      * @param region -
      * @returns falsy if the region is fine to try rendering. Otherwise,
-     *  return a react node + string of text.
-     *  string of text describes why it cannot be rendered
-     *  react node allows user to force load at current setting
+     * return a react node + string of text. string of text describes why it
+     * cannot be rendered react node allows user to force load at current
+     * setting
      */
     regionCannotBeRendered(): null;
 } & {

package/pluggableElementTypes/models/BaseDisplayModel.js

@@ -119,9 +119,9 @@ function stateModelFactory() {
          * #method
          * @param region -
          * @returns falsy if the region is fine to try rendering. Otherwise,
-         *  return a react node + string of text.
-         *  string of text describes why it cannot be rendered
-         *  react node allows user to force load at current setting
+         * return a react node + string of text. string of text describes why it
+         * cannot be rendered react node allows user to force load at current
+         * setting
          */
         regionCannotBeRendered( /* region */) {
             return null;

package/pluggableElementTypes/renderers/util/serializableFilterChain.js

@@ -3,7 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const jexlStrings_1 = require("../../../util/jexlStrings");
 class SerializableFilterChain {
     constructor({ filters = [] }) {
-        this.filterChain = filters.map(inputFilter => {
+        this.filterChain = filters
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map(inputFilter => {
             if (typeof inputFilter === 'string') {
                 const expr = (0, jexlStrings_1.stringToJexlExpression)(inputFilter);
                 return { expr, string: inputFilter };

package/rpc/methods/util.d.ts

@@ -1,4 +1,5 @@
-import ServerSideRendererType, { RenderArgs as ServerSideRenderArgs, RenderArgsSerialized as ServerSideRenderArgsSerialized } from '../../pluggableElementTypes/renderers/ServerSideRendererType';
+import { ServerSideRendererType } from '../../pluggableElementTypes';
+import { RenderArgs as ServerSideRenderArgs, RenderArgsSerialized as ServerSideRenderArgsSerialized } from '../../pluggableElementTypes/renderers/ServerSideRendererType';
 import { Region } from '../../util';
 export interface RenderArgs extends ServerSideRenderArgs {
     adapterConfig: {};
@@ -10,5 +11,5 @@ export interface RenderArgsSerialized extends ServerSideRenderArgsSerialized {
     adapterConfig: {};
     rendererType: string;
 }
-export declare function validateRendererType<T>(rendererType: string, RendererType: T): T & ServerSideRendererType;
+export declare function validateRendererType<T>(rendererType: string, RendererType: T): ServerSideRendererType;
 export { type RenderResults, type ResultsSerialized, } from '../../pluggableElementTypes/renderers/ServerSideRendererType';

package/rpc/methods/util.js

@@ -1,10 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.validateRendererType = void 0;
-const ServerSideRendererType_1 = __importDefault(require("../../pluggableElementTypes/renderers/ServerSideRendererType"));
 function validateRendererType(rendererType, RendererType) {
     if (!RendererType) {
         throw new Error(`renderer "${rendererType}" not found`);
@@ -13,9 +9,6 @@ function validateRendererType(rendererType, RendererType) {
     if (!RendererType.ReactComponent) {
         throw new Error(`renderer ${rendererType} has no ReactComponent, it may not be completely implemented yet`);
     }
-    if (!(RendererType instanceof ServerSideRendererType_1.default)) {
-        throw new TypeError('CoreRender requires a renderer that is a subclass of ServerSideRendererType');
-    }
     return RendererType;
 }
 exports.validateRendererType = validateRendererType;

package/stories/JBrowseCore.stories.d.ts

@@ -0,0 +1,5 @@
+export { CDSNoCoords, CDSCoords, GeneCoordsGenomic, GeneCollapsedIntronCoords, GeneCollapsedIntronNoCoords, } from './examples';
+declare const _default: {
+    title: string;
+};
+export default _default;

package/stories/JBrowseCore.stories.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GeneCollapsedIntronNoCoords = exports.GeneCollapsedIntronCoords = exports.GeneCoordsGenomic = exports.CDSCoords = exports.CDSNoCoords = void 0;
+var examples_1 = require("./examples");
+Object.defineProperty(exports, "CDSNoCoords", { enumerable: true, get: function () { return examples_1.CDSNoCoords; } });
+Object.defineProperty(exports, "CDSCoords", { enumerable: true, get: function () { return examples_1.CDSCoords; } });
+Object.defineProperty(exports, "GeneCoordsGenomic", { enumerable: true, get: function () { return examples_1.GeneCoordsGenomic; } });
+Object.defineProperty(exports, "GeneCollapsedIntronCoords", { enumerable: true, get: function () { return examples_1.GeneCollapsedIntronCoords; } });
+Object.defineProperty(exports, "GeneCollapsedIntronNoCoords", { enumerable: true, get: function () { return examples_1.GeneCollapsedIntronNoCoords; } });
+exports.default = { title: 'Source code for examples' };

package/stories/examples/WithSequencePanel.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+declare function GeneCollapsedIntronCoords(): React.JSX.Element;
+declare function GeneCollapsedIntronNoCoords(): React.JSX.Element;
+declare function CDSCoords(): React.JSX.Element;
+declare function GeneCoordsGenomic(): React.JSX.Element;
+declare function CDSNoCoords(): React.JSX.Element;
+export { CDSNoCoords, CDSCoords, GeneCoordsGenomic, GeneCollapsedIntronCoords, GeneCollapsedIntronNoCoords, };

package/stories/examples/WithSequencePanel.js

@@ -0,0 +1,43 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GeneCollapsedIntronNoCoords = exports.GeneCollapsedIntronCoords = exports.GeneCoordsGenomic = exports.CDSCoords = exports.CDSNoCoords = void 0;
+const react_1 = __importDefault(require("react"));
+const SequencePanel_1 = __importDefault(require(".././../BaseFeatureWidget/SequenceFeatureDetails/SequencePanel"));
+const model_1 = require(".././../BaseFeatureWidget/SequenceFeatureDetails/model");
+const util_1 = require("./util");
+function GeneCollapsedIntronCoords() {
+    const model = (0, model_1.SequenceFeatureDetailsF)().create();
+    model.setShowCoordinates('relative');
+    model.setMode('gene_collapsed_intron');
+    return react_1.default.createElement(SequencePanel_1.default, { model: model, sequence: util_1.sequence, feature: util_1.feature });
+}
+exports.GeneCollapsedIntronCoords = GeneCollapsedIntronCoords;
+function GeneCollapsedIntronNoCoords() {
+    const model = (0, model_1.SequenceFeatureDetailsF)().create();
+    model.setMode('gene_collapsed_intron');
+    return react_1.default.createElement(SequencePanel_1.default, { model: model, sequence: util_1.sequence, feature: util_1.feature });
+}
+exports.GeneCollapsedIntronNoCoords = GeneCollapsedIntronNoCoords;
+function CDSCoords() {
+    const model = (0, model_1.SequenceFeatureDetailsF)().create();
+    model.setShowCoordinates('relative');
+    model.setMode('cds');
+    return react_1.default.createElement(SequencePanel_1.default, { model: model, sequence: util_1.sequence, feature: util_1.feature });
+}
+exports.CDSCoords = CDSCoords;
+function GeneCoordsGenomic() {
+    const model = (0, model_1.SequenceFeatureDetailsF)().create();
+    model.setShowCoordinates('genomic');
+    model.setMode('gene');
+    return react_1.default.createElement(SequencePanel_1.default, { model: model, sequence: util_1.sequence, feature: util_1.feature });
+}
+exports.GeneCoordsGenomic = GeneCoordsGenomic;
+function CDSNoCoords() {
+    const model = (0, model_1.SequenceFeatureDetailsF)().create();
+    model.setMode('cds');
+    return react_1.default.createElement(SequencePanel_1.default, { model: model, sequence: util_1.sequence, feature: util_1.feature });
+}
+exports.CDSNoCoords = CDSNoCoords;

package/stories/examples/index.d.ts

@@ -0,0 +1 @@
+export * from './WithSequencePanel';

package/stories/examples/index.js

@@ -0,0 +1,17 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./WithSequencePanel"), exports);

package/stories/examples/util.d.ts

@@ -0,0 +1,33 @@
+export declare const feature: {
+    strand: number;
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    phase: number;
+    derived_features: never[];
+    refName: string;
+    id: string;
+    parent: string;
+    name: string;
+    note: string;
+    index: string;
+    subfeatures: {
+        strand: number;
+        source: string;
+        type: string;
+        start: number;
+        end: number;
+        phase: number;
+        derived_features: never[];
+        refName: string;
+        parent: string;
+        uniqueId: string;
+        parentId: string;
+    }[];
+    uniqueId: string;
+    parentId: string;
+};
+export declare const sequence: {
+    seq: string;
+};