@jbrowse/core 2.4.1 → 2.4.2

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -3,9 +3,7 @@ import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { BaseCardProps, BaseProps } from './types';
 import { SimpleFeatureSerializedNoId } from '../util/simpleFeature';
 export declare const useStyles: (params: void, styleOverrides?: {
-    props: {
-        classes?: Record<string, string> | undefined;
-    } & Record<string, unknown>;
+    props: any;
     ownerState?: Record<string, unknown> | undefined;
 } | undefined) => {
     classes: Record<"expansionPanelDetails" | "expandIcon" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue", string>;

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -48,9 +48,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
     formControl: {
         margin: 0,
     },
-    container: {
-        margin: theme.spacing(1),
-    },
     container2: {
         marginTop: theme.spacing(1),
     },
@@ -60,14 +57,10 @@ const BPLIMIT = 500000;
 // sequence. this is a best effort and weird genomic phenomena could lead these
 // to not be 100% accurate
 function SequenceFeatureDetails({ model, feature }) {
-    var _a;
     const { classes } = useStyles();
-    const parentFeature = feature;
-    const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
-    const isGene = feature.type === 'gene';
     const [shown, setShown] = (0, react_1.useState)(false);
     const [helpShown, setHelpShown] = (0, react_1.useState)(false);
-    return (isGene && !hasCDS) || !model ? null : (react_1.default.createElement("div", { className: classes.container2 },
+    return !model ? null : (react_1.default.createElement("div", { className: classes.container2 },
         react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence'),
         react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
             react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpShown(true) },
@@ -79,7 +72,7 @@ function SequenceFeatureDetails({ model, feature }) {
 }
 exports.default = SequenceFeatureDetails;
 function FeatureSequence({ model, feature }) {
-    var _a;
+    var _a, _b;
     const { classes } = useStyles();
     const parentFeature = feature;
     const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
@@ -166,7 +159,7 @@ function FeatureSequence({ model, feature }) {
     // only attempt fetching gene type sequence on a bare CDS if it has no parent
     const attemptGeneType = feature.type === 'CDS'
         ? sequenceTypes.includes('CDS') && !feature.parentId
-        : sequenceTypes.includes(feature.type);
+        : sequenceTypes.includes(feature.type) && ((_b = feature.subfeatures) === null || _b === void 0 ? void 0 : _b.length);
     const val = attemptGeneType ? (hasCDS ? 'cds' : 'cdna') : 'genomic';
     // this useEffect is needed to reset the mode/setMode useState because the
     // contents of the select box can completely change depending on whether we

package/BaseFeatureWidget/index.d.ts

@@ -28,8 +28,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>>, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/BaseFeatureWidget/index.js

@@ -60,20 +60,17 @@ function stateModelFactory(pluginManager) {
                 const session = (0, util_1.getSession)(self);
                 if (unformattedFeatureData) {
                     const feature = (0, clone_1.default)(unformattedFeatureData);
-                    const f = (obj, arg2) => (0, configuration_1.getConf)(obj, ['formatDetails', arg2], { feature });
+                    const combine = (arg2, feature) => ({
+                        ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
+                        ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
+                    });
                     if (track) {
                         // eslint-disable-next-line no-underscore-dangle
-                        feature.__jbrowsefmt = {
-                            ...f(session, 'feature'),
-                            ...f(track, 'feature'),
-                        };
+                        feature.__jbrowsefmt = combine('feature', feature);
                         const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
                         formatSubfeatures(feature, depth, sub => {
                             // eslint-disable-next-line no-underscore-dangle
-                            sub.__jbrowsefmt = {
-                                ...f(session, 'subfeature'),
-                                ...f(track, 'subfeature'),
-                            };
+                            sub.__jbrowsefmt = combine('subfeatures', sub);
                         });
                     }
                     self.setFormattedData(feature);

package/PluginManager.d.ts

@@ -228,9 +228,7 @@ export default class PluginManager {
                 name?: string | Record<string, unknown> | undefined;
                 uniqId?: string | undefined;
             } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-                props: {
-                    classes?: Record<string, string> | undefined;
-                } & Record<string, unknown>;
+                props: any;
                 ownerState?: Record<string, unknown> | undefined;
             } | undefined) => {
                 classes: Record<RuleName, string>;

package/ReExports/modules.d.ts

@@ -145,9 +145,7 @@ declare const libs: {
             name?: string | Record<string, unknown> | undefined;
             uniqId?: string | undefined;
         } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-            props: {
-                classes?: Record<string, string> | undefined;
-            } & Record<string, unknown>;
+            props: any;
             ownerState?: Record<string, unknown> | undefined;
         } | undefined) => {
             classes: Record<RuleName, string>;

package/configuration/configurationSchema.d.ts

@@ -1,5 +1,5 @@
 import { Instance, IAnyType } from 'mobx-state-tree';
-import { ConfigSlotDefinition } from './configurationSlot';
+import ConfigSlot, { ConfigSlotDefinition } from './configurationSlot';
 export interface ConfigurationSchemaDefinition {
     [n: string]: ConfigSlotDefinition | ConfigurationSchemaDefinition | string | number | IAnyType;
 }
@@ -23,6 +23,8 @@ export interface AnyConfigurationSchemaType extends ReturnType<typeof makeConfig
     type: string;
 }
 export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>;
+export type AnyConfigurationSlotType = ReturnType<typeof ConfigSlot>;
+export type AnyConfigurationSlot = Instance<AnyConfigurationSlotType>;
 export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> = Instance<SCHEMA>;
 export declare function ConfigurationSchema<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions>(modelName: string, inputSchemaDefinition: DEFINITION, inputOptions?: OPTIONS): AnyConfigurationSchemaType;
 export declare function ConfigurationReference(schemaType: IAnyType): import("mobx-state-tree").ITypeUnion<any, any, any>;

package/configuration/configurationSlot.d.ts

@@ -1,5 +1,6 @@
 import { IAnyModelType, IAnyComplexType } from 'mobx-state-tree';
 export interface ConfigSlotDefinition {
+    /** human-readable description of the slot's meaning */
     description?: string;
     /** custom base MST model for the slot's value */
     model?: IAnyModelType | IAnyComplexType;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.4.1",
+  "version": "2.4.2",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -54,7 +54,6 @@
     "material-ui-popup-state": "^5.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-use-measure": "^2.1.1",
     "serialize-error": "^8.0.0",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0"
@@ -75,5 +74,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
+  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
 }

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -158,7 +158,7 @@ function createBaseTrackConfig(pluginManager) {
                 if (!type) {
                     throw new Error(`unknown display type ${type}`);
                 }
-                const display = self.displays.find((d) => d && d.displayId === conf.displayId);
+                const display = self.displays.find((d) => (d === null || d === void 0 ? void 0 : d.displayId) === conf.displayId);
                 if (display) {
                     return display;
                 }