@jbrowse/core 2.11.0 → 2.11.2

package/BaseFeatureWidget/SequenceFeatureDetails/model.js

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SequenceFeatureDetailsF = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+// locals
+const util_1 = require("../../util");
+function SequenceFeatureDetailsF() {
+    return mobx_state_tree_1.types
+        .model('SequenceFeatureDetails', {})
+        .volatile(() => {
+        var _a, _b;
+        return ({
+            intronBp: +((_a = (0, util_1.localStorageGetItem)('sequenceFeatureDetails-intronBp')) !== null && _a !== void 0 ? _a : 10),
+            upDownBp: +((_b = (0, util_1.localStorageGetItem)('sequenceFeatureDetails-upDownBp')) !== null && _b !== void 0 ? _b : 100),
+            upperCaseCDS: Boolean(JSON.parse((0, util_1.localStorageGetItem)('sequenceFeatureDetails-upperCaseCDS') || 'true')),
+        });
+    })
+        .actions(self => ({
+        setUpDownBp(f) {
+            self.upDownBp = f;
+        },
+        setIntronBp(f) {
+            self.intronBp = f;
+        },
+        setUpperCaseCDS(f) {
+            self.upperCaseCDS = f;
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-upDownBp', JSON.stringify(self.upDownBp));
+                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-intronBp', JSON.stringify(self.intronBp));
+                (0, util_1.localStorageSetItem)('sequenceFeatureDetails-upperCaseCDS', JSON.stringify(self.upperCaseCDS));
+            }));
+        },
+    }));
+}
+exports.SequenceFeatureDetailsF = SequenceFeatureDetailsF;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts

@@ -0,0 +1,15 @@
+import React from 'react';
+import { Feat } from '../../util';
+import { SequenceFeatureDetailsModel } from '../model';
+declare const CDNASequence: ({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, model, }: {
+    utr: Feat[];
+    cds: Feat[];
+    exons: Feat[];
+    sequence: string;
+    upstream?: string;
+    downstream?: string;
+    includeIntrons?: boolean;
+    collapseIntron?: boolean;
+    model: SequenceFeatureDetailsModel;
+}) => React.JSX.Element;
+export default CDNASequence;

package/BaseFeatureWidget/SequenceFeatureDetails/{CDNASequence.js → seqtypes/CDNASequence.js}

@@ -4,22 +4,31 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-function CDNASequence({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }) {
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("../util");
+const CDNASequence = (0, mobx_react_1.observer)(function ({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, model, }) {
+    const { upperCaseCDS, intronBp } = model;
+    const hasCds = cds.length > 0;
     const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
+    const toLower = (s) => (upperCaseCDS ? s.toLowerCase() : s);
+    const toUpper = (s) => (upperCaseCDS ? s.toUpperCase() : s);
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, upstream)) : null,
+        upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, toLower(upstream))) : null,
         chunks.map((chunk, idx) => {
             var _a;
             const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
             return (react_1.default.createElement(react_1.default.Fragment, { key: JSON.stringify(chunk) },
                 react_1.default.createElement("span", { style: {
                         background: chunk.type === 'CDS' ? util_1.cdsColor : util_1.utrColor,
-                    } }, sequence.slice(chunk.start, chunk.end)),
-                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: util_1.intronColor } }, collapseIntron && intron.length > intronBp * 2
+                    } }, hasCds
+                    ? chunk.type === 'CDS'
+                        ? toUpper(sequence.slice(chunk.start, chunk.end))
+                        : toLower(sequence.slice(chunk.start, chunk.end))
+                    : toUpper(sequence.slice(chunk.start, chunk.end))),
+                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: util_1.intronColor } }, toLower(collapseIntron && intron.length > intronBp * 2
                     ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
-                    : intron)) : null));
+                    : intron))) : null));
         }),
-        downstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, downstream)) : null));
-}
+        downstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, toLower(downstream))) : null));
+});
 exports.default = CDNASequence;

package/BaseFeatureWidget/SequenceFeatureDetails/{CDSSequence.d.ts → seqtypes/CDSSequence.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feat } from '../util';
+import { Feat } from '../../util';
 export default function CDSSequence({ cds, sequence, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/{CDSSequence.js → seqtypes/CDSSequence.js}

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-const util_2 = require("../util");
+const util_1 = require("../util");
+const util_2 = require("../../util");
 function CDSSequence({ cds, sequence, }) {
     return react_1.default.createElement("span", { style: { background: util_1.cdsColor } }, (0, util_2.stitch)(cds, sequence));
 }

package/BaseFeatureWidget/SequenceFeatureDetails/{GenomicSequence.js → seqtypes/GenomicSequence.js}

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
+const util_1 = require("../util");
 function GenomicSequence({ sequence, upstream, downstream, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, upstream)) : null,

package/BaseFeatureWidget/SequenceFeatureDetails/{ProteinSequence.d.ts → seqtypes/ProteinSequence.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feat } from '../util';
+import { Feat } from '../../util';
 export default function ProteinSequence({ cds, sequence, codonTable, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/{ProteinSequence.js → seqtypes/ProteinSequence.js}

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("../util");
-const util_2 = require("./util");
+const util_1 = require("../../util");
+const util_2 = require("../util");
 function ProteinSequence({ cds, sequence, codonTable, }) {
     const str = (0, util_1.stitch)(cds, sequence);
     let protein = '';

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -1,3 +1,4 @@
+import { Instance } from 'mobx-state-tree';
 import PluginManager from '../PluginManager';
 /**
  * #stateModel BaseFeatureWidget
@@ -47,6 +48,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     error: unknown;
 } & {
@@ -113,6 +128,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>>, {
     id: string;
     type: "BaseFeatureWidget";
@@ -122,5 +151,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 }>;
+export type BaseFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
+export type BaseFeatureWidgetModel = Instance<BaseFeatureWidgetStateModel>;

package/BaseFeatureWidget/stateModelFactory.js

@@ -10,6 +10,7 @@ const clone_1 = __importDefault(require("clone"));
 const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 const mst_1 = require("../util/types/mst");
+const model_1 = require("./SequenceFeatureDetails/model");
 function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
     var _a;
     if (depth <= currentDepth) {
@@ -70,6 +71,10 @@ function stateModelFactory(pluginManager) {
          * #property
          */
         maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+        /**
+         * #property
+         */
+        sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
     })
         .volatile(() => ({
         error: undefined,

package/BaseFeatureWidget/types.d.ts

@@ -1,16 +1,11 @@
 import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
-import { AbstractViewModel } from '../util';
+import { BaseFeatureWidgetModel } from './stateModelFactory';
 export interface BaseProps extends BaseCardProps {
     feature: SimpleFeatureSerialized;
     formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
-    model?: IAnyStateTreeNode & {
-        view?: AbstractViewModel & {
-            assemblyNames?: string[];
-        };
-    };
+    model?: BaseFeatureWidgetModel;
 }
 export interface BaseCardProps {
     title?: string;

package/BaseFeatureWidget/util.d.ts

@@ -1,7 +1,7 @@
 export interface Feat {
     start: number;
     end: number;
-    type: string;
+    type?: string;
     name?: string;
     id?: string;
 }
@@ -25,7 +25,7 @@ export declare function dedupe(list: Feat[]): Feat[];
 export declare function revlist(list: Feat[], seqlen: number): {
     start: number;
     end: number;
-    type: string;
+    type?: string | undefined;
     name?: string | undefined;
     id?: string | undefined;
 }[];
@@ -33,6 +33,8 @@ export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
     type: string;
     start: number;
     end: number;
+    name?: string | undefined;
+    id?: string | undefined;
 }[];
 export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
     type: string;

package/PluginManager.d.ts

@@ -230,7 +230,7 @@ export default class PluginManager {
         '@mui/x-data-grid': {
             useGridApiContext: typeof import("@mui/x-data-grid").useGridApiContext;
             useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("react").MutableRefObject<Api>;
-            useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
+            useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps<any>;
         };
         '@mui/material/utils': typeof import("@mui/material/utils");
         '@material-ui/core/utils': typeof import("@mui/material/utils");

package/ReExports/modules.d.ts

@@ -138,7 +138,7 @@ declare const libs: {
     '@mui/x-data-grid': {
         useGridApiContext: typeof useGridApiContext;
         useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
-        useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
+        useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps<any>;
     };
     '@mui/material/utils': typeof MUIUtils;
     '@material-ui/core/utils': typeof MUIUtils;

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/data_adapters/CytobandAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '../../PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CytobandAdapterF(pluginManager: PluginManager): void;

package/data_adapters/CytobandAdapter/index.js

@@ -28,10 +28,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("../../pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function CytobandAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
         name: 'CytobandAdapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CytobandAdapter'))).then(f => f.default),
     }));
-};
+}
+exports.default = CytobandAdapterF;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -31,6 +31,7 @@
     "@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 +59,6 @@
   },
   "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 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }

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;