@jbrowse/core 2.11.2 → 2.12.0

package/ui/Dialog.js

@@ -12,6 +12,7 @@ const react_error_boundary_1 = require("react-error-boundary");
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 // locals
 const ErrorMessage_1 = __importDefault(require("./ErrorMessage"));
+const SanitizedHTML_1 = __importDefault(require("./SanitizedHTML"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     closeButton: {
         position: 'absolute',
@@ -31,7 +32,7 @@ const Dialog = (0, mobx_react_1.observer)(function (props) {
     return (react_1.default.createElement(material_1.Dialog, { ...props },
         react_1.default.createElement(material_1.ScopedCssBaseline, null,
             react_1.default.isValidElement(header) ? (header) : (react_1.default.createElement(material_1.DialogTitle, null,
-                title,
+                react_1.default.createElement(SanitizedHTML_1.default, { html: title || '' }),
                 onClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => {
                         // @ts-expect-error
                         onClose();

package/util/Base1DUtils.d.ts

@@ -19,7 +19,7 @@ export declare function pxToBp(self: ViewSnap, px: number): {
     offset: number;
     start: number;
     end: number;
-    reversed: boolean;
+    reversed?: boolean;
 };
 export declare function bpToPx({ refName, coord, regionNumber, self, }: {
     refName: string;

package/util/Base1DUtils.js

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.bpToPxMap = exports.bpToPx = exports.pxToBp = exports.moveTo = void 0;
-const mobx_state_tree_1 = require("mobx-state-tree");
 function lengthBetween(self, start, end) {
     let bpSoFar = 0;
     const { displayedRegions } = self;
@@ -69,8 +68,7 @@ function pxToBp(self, px) {
     const bp = (offsetPx + px) * bpPerPx;
     if (bp < 0) {
         const r = displayedRegions[0];
-        const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-        // @ts-expect-error
+        const snap = r;
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
@@ -87,8 +85,7 @@ function pxToBp(self, px) {
         const len = r.end - r.start;
         const offset = bp - bpSoFar;
         if (len + bpSoFar > bp && bpSoFar <= bp) {
-            const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-            // @ts-expect-error
+            const snap = r;
             return {
                 // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
                 ...snap,
@@ -112,8 +109,7 @@ function pxToBp(self, px) {
         const r = displayedRegions.at(-1);
         const len = r.end - r.start;
         const offset = bp - bpSoFar + len;
-        const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-        // @ts-expect-error
+        const snap = r;
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,

package/util/Base1DViewModel.d.ts

@@ -4,16 +4,7 @@ import { Region as IRegion } from './types';
 import { BpOffset } from './Base1DUtils';
 declare const Base1DView: 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<IRegion[], IRegion[], IRegion[]>, [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]>;
@@ -78,16 +69,14 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
      */
     pxToBp(px: number): {
         coord: number;
-        index: number; /**
-         * #getter
-         */
+        index: number;
         refName: string;
         oob: boolean;
         assemblyName: string;
         offset: number;
         start: number;
         end: number;
-        reversed: boolean;
+        reversed?: boolean | undefined;
     };
     /**
      * #method
@@ -136,8 +125,8 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
 } & {
     /**
      * #action
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
+     * offset is the base-pair-offset in the displayed region, index is the
+     * index of the displayed region in the linear genome view
      *
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`

package/util/Base1DViewModel.js

@@ -24,7 +24,7 @@ const Base1DView = mobx_state_tree_1.types
     /**
      * #property
      */
-    displayedRegions: mobx_state_tree_1.types.array(mst_1.Region),
+    displayedRegions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
     /**
      * #property
      */
@@ -77,9 +77,7 @@ const Base1DView = mobx_state_tree_1.types
      * #getter
      */
     get assemblyNames() {
-        return [
-            ...new Set(self.displayedRegions.map(region => region.assemblyName)),
-        ];
+        return [...new Set(self.displayedRegions.map(r => r.assemblyName))];
     },
     /**
      * #getter
@@ -107,9 +105,7 @@ const Base1DView = mobx_state_tree_1.types
      * #getter
      */
     get totalBp() {
-        return self.displayedRegions
-            .map(a => a.end - a.start)
-            .reduce((a, b) => a + b, 0);
+        return (0, index_1.sum)(self.displayedRegions.map(a => a.end - a.start));
     },
 }))
     .views(self => ({
@@ -129,9 +125,7 @@ const Base1DView = mobx_state_tree_1.types
      * #getter
      */
     get currBp() {
-        return this.dynamicBlocks
-            .map(a => a.end - a.start)
-            .reduce((a, b) => a + b, 0);
+        return (0, index_1.sum)(this.dynamicBlocks.map(a => a.end - a.start));
     },
 }))
     .views(self => ({
@@ -230,8 +224,8 @@ const Base1DView = mobx_state_tree_1.types
     .actions(self => ({
     /**
      * #action
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
+     * offset is the base-pair-offset in the displayed region, index is the
+     * index of the displayed region in the linear genome view
      *
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`

package/util/index.d.ts

@@ -337,7 +337,7 @@ export interface ViewSnap {
         start: number;
         end: number;
         refName: string;
-        reversed: boolean;
+        reversed?: boolean;
         assemblyName: string;
     })[];
 }

package/util/tracks.d.ts

@@ -4,11 +4,12 @@ import { AnyConfigurationModel } from '../configuration';
 export declare function getTrackAssemblyNames(track: IAnyStateTreeNode & {
     configuration: AnyConfigurationModel;
 }): string[];
+export declare function getConfAssemblyNames(conf: AnyConfigurationModel): string[];
 /** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
 export declare function getRpcSessionId(thisNode: IAnyStateTreeNode): string;
 /**
- * given an MST node, get the renderprops of the first parent container that has
- * renderProps
+ * given an MST node, get the renderprops of the first parent container that
+ * has renderProps
  * @param node -
  * @returns renderprops, or empty object if none found
  */

package/util/tracks.js

@@ -1,23 +1,27 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrackName = exports.generateUnknownTrackConf = exports.generateUnsupportedTrackConf = exports.guessTrackType = exports.guessAdapter = exports.getFileName = exports.makeIndexType = exports.makeIndex = exports.storeBlobLocation = exports.setBlobMap = exports.getBlobMap = exports.getBlob = exports.UNSUPPORTED = exports.UNKNOWN = exports.getParentRenderProps = exports.getRpcSessionId = exports.getTrackAssemblyNames = void 0;
+exports.getTrackName = exports.generateUnknownTrackConf = exports.generateUnsupportedTrackConf = exports.guessTrackType = exports.guessAdapter = exports.getFileName = exports.makeIndexType = exports.makeIndex = exports.storeBlobLocation = exports.setBlobMap = exports.getBlobMap = exports.getBlob = exports.UNSUPPORTED = exports.UNKNOWN = exports.getParentRenderProps = exports.getRpcSessionId = exports.getConfAssemblyNames = exports.getTrackAssemblyNames = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const index_1 = require("./index");
 const configuration_1 = require("../configuration");
 /* utility functions for use by track models and so forth */
 function getTrackAssemblyNames(track) {
-    const trackAssemblyNames = (0, configuration_1.getConf)(track, 'assemblyNames');
+    return getConfAssemblyNames(track.configuration);
+}
+exports.getTrackAssemblyNames = getTrackAssemblyNames;
+function getConfAssemblyNames(conf) {
+    const trackAssemblyNames = (0, configuration_1.readConfObject)(conf, 'assemblyNames');
     if (!trackAssemblyNames) {
         // Check if it's an assembly sequence track
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const parent = (0, mobx_state_tree_1.getParent)(track.configuration);
+        const parent = (0, mobx_state_tree_1.getParent)(conf);
         if ('sequence' in parent) {
             return [(0, configuration_1.readConfObject)(parent, 'name')];
         }
     }
     return trackAssemblyNames;
 }
-exports.getTrackAssemblyNames = getTrackAssemblyNames;
+exports.getConfAssemblyNames = getConfAssemblyNames;
 /** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
 function getRpcSessionId(thisNode) {
     let highestRpcSessionId;
@@ -34,8 +38,8 @@ function getRpcSessionId(thisNode) {
 }
 exports.getRpcSessionId = getRpcSessionId;
 /**
- * given an MST node, get the renderprops of the first parent container that has
- * renderProps
+ * given an MST node, get the renderprops of the first parent container that
+ * has renderProps
  * @param node -
  * @returns renderprops, or empty object if none found
  */

package/util/types/index.d.ts

@@ -225,7 +225,10 @@ export interface AbstractMenuManager {
 export declare function isAbstractMenuManager(thing: unknown): thing is AbstractMenuManager;
 export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion> {
 }
-/** a description of a specific genomic region. assemblyName, refName, start, end, and reversed */
+/**
+ * a description of a specific genomic region. assemblyName, refName, start,
+ * end, and reversed
+ */
 export interface Region extends SnapshotIn<typeof MUIRegion> {
 }
 export interface AugmentedRegion extends Region {

package/ui/useResizeBar.d.ts

@@ -1,5 +0,0 @@
-/// <reference types="react" />
-export declare function useResizeBar(): {
-    ref: import("react").RefObject<HTMLDivElement>;
-    scrollLeft: number;
-};

package/ui/useResizeBar.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.useResizeBar = void 0;
-const react_1 = require("react");
-function useResizeBar() {
-    const ref = (0, react_1.useRef)(null);
-    const [scrollLeft, setScrollLeft] = (0, react_1.useState)(0);
-    (0, react_1.useEffect)(() => {
-        const timer = setInterval(() => {
-            var _a;
-            const elt = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.querySelector('.MuiDataGrid-virtualScroller');
-            if (elt) {
-                setScrollLeft(elt.scrollLeft);
-            }
-        }, 100);
-        return () => {
-            clearInterval(timer);
-        };
-    }, []);
-    return { ref, scrollLeft };
-}
-exports.useResizeBar = useResizeBar;