@jbrowse/plugin-linear-genome-view 2.13.0 → 2.14.0

package/dist/LinearGenomeView/components/hooks.js

@@ -45,7 +45,7 @@ function useSideScroll(model) {
             };
         }
         return cleanup;
-    }, [model, mouseDragging, prevX]);
+    }, [model, mouseDragging]);
     function mouseDown(event) {
         if (event.shiftKey) {
             return;
@@ -122,7 +122,7 @@ function useRangeSelect(ref, model, shiftOnly) {
             };
         }
         return () => { };
-    }, [startX, mouseDragging, anchorPosition, model, ref]);
+    }, [startX, mouseDragging, model, ref]);
     (0, react_1.useEffect)(() => {
         if (!mouseDragging &&
             currentX !== undefined &&
@@ -178,29 +178,27 @@ function useRangeSelect(ref, model, shiftOnly) {
             handleMenuItemClick,
         };
     }
-    else {
-        const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
-        const left = right < startX ? right : startX;
-        const width = Math.abs(right - startX);
-        const leftBpOffset = model.pxToBp(left);
-        const rightBpOffset = model.pxToBp(left + width);
-        const numOfBpSelected = Math.ceil(width * model.bpPerPx);
-        return {
-            open,
-            rubberbandOn: true,
-            mouseDown,
-            mouseMove,
-            mouseOut,
-            handleClose,
-            handleMenuItemClick,
-            leftBpOffset,
-            rightBpOffset,
-            anchorPosition,
-            numOfBpSelected,
-            width,
-            left,
-        };
-    }
+    const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
+    const left = right < startX ? right : startX;
+    const width = Math.abs(right - startX);
+    const leftBpOffset = model.pxToBp(left);
+    const rightBpOffset = model.pxToBp(left + width);
+    const numOfBpSelected = Math.ceil(width * model.bpPerPx);
+    return {
+        open,
+        rubberbandOn: true,
+        mouseDown,
+        mouseMove,
+        mouseOut,
+        handleClose,
+        handleMenuItemClick,
+        leftBpOffset,
+        rightBpOffset,
+        anchorPosition,
+        numOfBpSelected,
+        width,
+        left,
+    };
 }
 function useWheelScroll(ref, model) {
     const delta = (0, react_1.useRef)(0);
@@ -211,7 +209,7 @@ function useWheelScroll(ref, model) {
         // if ctrl is held down, zoom in with y-scroll
         // else scroll horizontally with x-scroll
         function onWheel(event) {
-            if (event.ctrlKey === true) {
+            if (event.ctrlKey) {
                 event.preventDefault();
                 delta.current += event.deltaY / 500;
                 model.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));

package/dist/LinearGenomeView/components/util.d.ts

@@ -12,10 +12,10 @@ export declare function fetchResults({ queryString, searchType, searchScope, ran
     assembly?: Assembly;
 }): Promise<BaseResult[]>;
 export declare function splitLast(str: string, split: string): [string, string];
-export declare function getRelativeX<T extends {
+export declare function getRelativeX(event: {
     clientX: number;
     target: EventTarget | null;
-}>(event: T, element: HTMLElement | null): number;
+}, element: HTMLElement | null): number;
 export declare function getCytobands(assembly: Assembly | undefined, refName: string): {
     refName: string;
     start: number;

package/dist/LinearGenomeView/model.d.ts

@@ -33,6 +33,12 @@ export interface ExportSvgOptions {
     trackLabels?: string;
     themeName?: string;
 }
+export interface HighlightType {
+    start: number;
+    end: number;
+    assemblyName: string;
+    refName: string;
+}
 export interface NavLocation {
     refName: string;
     start?: number;
@@ -72,8 +78,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
+    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
 } & {
@@ -87,7 +94,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     minimumBlockWidth: number;
     draggingTrackId: undefined | string;
     volatileError: unknown;
-    afterDisplayedRegionsSetCallbacks: Function[];
+    afterDisplayedRegionsSetCallbacks: (() => void)[];
     scaleFactor: number;
     trackRefs: Record<string, HTMLDivElement>;
     coarseDynamicBlocks: BaseBlock[];
@@ -95,7 +102,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     leftOffset: undefined | BpOffset;
     rightOffset: undefined | BpOffset;
 } & {
-    scaleBarDisplayPrefix(): "";
     /**
      * #getter
      * this is the effective value of the track labels setting, incorporating
@@ -115,6 +121,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly assemblyNames: string[];
 } & {
+    /**
+     * #method
+     */
+    scaleBarDisplayPrefix(): string | undefined;
     /**
      * #method
      */
@@ -174,7 +184,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly error: {};
+    readonly error: unknown;
     /**
      * #getter
      */
@@ -217,6 +227,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly trackTypeActions: Map<string, MenuItem[]>;
 } & {
+    /**
+     * #action
+     */
+    setShowTrackOutlines(arg: boolean): void;
     /**
      * #action
      */
@@ -252,15 +266,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    addToHighlights(highlight: Required<ParsedLocString>): void;
+    addToHighlights(highlight: HighlightType): void;
     /**
      * #action
      */
-    setHighlight(highlight: Required<ParsedLocString>[] | undefined): void;
+    setHighlight(highlight?: HighlightType[]): void;
     /**
      * #action
      */
-    removeHighlight(highlight: Required<ParsedLocString>): void;
+    removeHighlight(highlight: HighlightType): void;
     /**
      * #action
      */
@@ -317,10 +331,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     moveTrack(movingId: string, targetId: string): void;
-    /**
-     * #action
-     */
-    closeView(): void;
     /**
      * #action
      */
@@ -372,7 +382,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * schedule something to be run after the next time displayedRegions is
      * set
      */
-    afterDisplayedRegionsSet(cb: Function): void;
+    afterDisplayedRegionsSet(cb: () => void): void;
     /**
      * #action
      */
@@ -614,8 +624,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
+    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }>>, import("mobx-state-tree")._NotCustomized>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;

package/dist/LinearGenomeView/model.js

@@ -177,6 +177,11 @@ function stateModelFactory(pluginManager) {
          * color by CDS
          */
         colorByCDS: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => Boolean(JSON.parse((0, util_1.localStorageGetItem)('lgv-colorByCDS') || 'false'))),
+        /**
+         * #property
+         * color by CDS
+         */
+        showTrackOutlines: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => Boolean(JSON.parse((0, util_1.localStorageGetItem)('lgv-showTrackOutlines') || 'true'))),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -194,9 +199,6 @@ function stateModelFactory(pluginManager) {
         rightOffset: undefined,
     }))
         .views(self => ({
-        scaleBarDisplayPrefix() {
-            return '';
-        },
         /**
          * #getter
          * this is the effective value of the track labels setting, incorporating
@@ -237,14 +239,20 @@ function stateModelFactory(pluginManager) {
         /**
          * #method
          */
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        scaleBarDisplayPrefix() {
+            return (0, mobx_state_tree_1.getParent)(self, 2).type === 'LinearSyntenyView'
+                ? self.assemblyNames[0]
+                : '';
+        },
+        /**
+         * #method
+         */
         MiniControlsComponent() {
             return MiniControls_1.default;
         },
         /**
          * #method
          */
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         HeaderComponent() {
             return Header_1.default;
         },
@@ -253,8 +261,7 @@ function stateModelFactory(pluginManager) {
          */
         get assemblyErrors() {
             const { assemblyManager } = (0, util_1.getSession)(self);
-            const { assemblyNames } = self;
-            return assemblyNames
+            return self.assemblyNames
                 .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
                 .filter(f => !!f)
                 .join(', ');
@@ -441,6 +448,12 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setShowTrackOutlines(arg) {
+            self.showTrackOutlines = arg;
+        },
         /**
          * #action
          */
@@ -493,8 +506,7 @@ function stateModelFactory(pluginManager) {
          * #action
          */
         addToHighlights(highlight) {
-            var _a;
-            (_a = self.highlight) === null || _a === void 0 ? void 0 : _a.push(highlight);
+            self.highlight.push(highlight);
         },
         /**
          * #action
@@ -622,7 +634,9 @@ function stateModelFactory(pluginManager) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
             const t = self.tracks.filter(t => t.configuration === conf);
-            (0, mobx_1.transaction)(() => t.forEach(t => self.tracks.remove(t)));
+            (0, mobx_1.transaction)(() => {
+                t.forEach(t => self.tracks.remove(t));
+            });
             return t.length;
         },
     }))
@@ -684,22 +698,6 @@ function stateModelFactory(pluginManager) {
             tracks.splice(newIndex, 0, self.tracks[oldIndex]);
             self.tracks = (0, mobx_state_tree_1.cast)(tracks);
         },
-        /**
-         * #action
-         */
-        closeView() {
-            const parent = (0, util_1.getContainingView)(self);
-            if (parent) {
-                // I am embedded in a some other view
-                if ((0, util_1.isViewContainer)(parent)) {
-                    parent.removeView(self);
-                }
-            }
-            else {
-                // I am part of a session
-                (0, util_1.getSession)(self).removeView(self);
-            }
-        },
         /**
          * #action
          */
@@ -932,8 +930,9 @@ function stateModelFactory(pluginManager) {
          * that offset is calculated manually with this method
          */
         get cytobandOffset() {
+            var _a;
             return this.showCytobands
-                ? (0, util_1.measureText)(self.displayedRegions[0].refName, 12) + 15
+                ? (0, util_1.measureText)(((_a = self.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.refName) || '', 12) + 15
                 : 0;
         },
     }))
@@ -995,7 +994,9 @@ function stateModelFactory(pluginManager) {
                     type: 'checkbox',
                     checked: self.colorByCDS,
                     icon: Palette_1.default,
-                    onClick: () => self.setColorByCDS(!self.colorByCDS),
+                    onClick: () => {
+                        self.setColorByCDS(!self.colorByCDS);
+                    },
                 },
                 {
                     label: 'Show...',
@@ -1009,32 +1010,50 @@ function stateModelFactory(pluginManager) {
                             label: 'Show center line',
                             type: 'checkbox',
                             checked: self.showCenterLine,
-                            onClick: () => self.setShowCenterLine(!self.showCenterLine),
+                            onClick: () => {
+                                self.setShowCenterLine(!self.showCenterLine);
+                            },
                         },
                         {
                             label: 'Show header',
                             type: 'checkbox',
                             checked: !self.hideHeader,
-                            onClick: () => self.setHideHeader(!self.hideHeader),
+                            onClick: () => {
+                                self.setHideHeader(!self.hideHeader);
+                            },
+                        },
+                        {
+                            label: 'Show track outlines',
+                            type: 'checkbox',
+                            checked: self.showTrackOutlines,
+                            onClick: () => {
+                                self.setShowTrackOutlines(!self.showTrackOutlines);
+                            },
                         },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',
                             checked: !self.hideHeaderOverview,
-                            onClick: () => self.setHideHeaderOverview(!self.hideHeaderOverview),
+                            onClick: () => {
+                                self.setHideHeaderOverview(!self.hideHeaderOverview);
+                            },
                             disabled: self.hideHeader,
                         },
                         {
                             label: 'Show no tracks active button',
                             type: 'checkbox',
                             checked: !self.hideNoTracksActive,
-                            onClick: () => self.setHideNoTracksActive(!self.hideNoTracksActive),
+                            onClick: () => {
+                                self.setHideNoTracksActive(!self.hideNoTracksActive);
+                            },
                         },
                         {
                             label: 'Show guidelines',
                             type: 'checkbox',
                             checked: self.showGridlines,
-                            onClick: () => self.setShowGridlines(!self.showGridlines),
+                            onClick: () => {
+                                self.setShowGridlines(!self.showGridlines);
+                            },
                         },
                         ...(canShowCytobands
                             ? [
@@ -1042,7 +1061,9 @@ function stateModelFactory(pluginManager) {
                                     label: 'Show ideogram',
                                     type: 'checkbox',
                                     checked: self.showCytobands,
-                                    onClick: () => self.setShowCytobands(!showCytobands),
+                                    onClick: () => {
+                                        self.setShowCytobands(!showCytobands);
+                                    },
                                 },
                             ]
                             : []),
@@ -1057,21 +1078,27 @@ function stateModelFactory(pluginManager) {
                             icon: Visibility_1.default,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'overlapping',
-                            onClick: () => self.setTrackLabels('overlapping'),
+                            onClick: () => {
+                                self.setTrackLabels('overlapping');
+                            },
                         },
                         {
                             label: 'Offset',
                             icon: Visibility_1.default,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'offset',
-                            onClick: () => self.setTrackLabels('offset'),
+                            onClick: () => {
+                                self.setTrackLabels('offset');
+                            },
                         },
                         {
                             label: 'Hidden',
                             icon: Visibility_1.default,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'hidden',
-                            onClick: () => self.setTrackLabels('hidden'),
+                            onClick: () => {
+                                self.setTrackLabels('hidden');
+                            },
                         },
                     ],
                 },
@@ -1192,13 +1219,11 @@ function stateModelFactory(pluginManager) {
         async navToLocString(input, optAssemblyName) {
             const { assemblyNames } = self;
             const { assemblyManager } = (0, util_1.getSession)(self);
-            const { isValidRefName } = assemblyManager;
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
-                // wait before isValidRefName can be called
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, isValidRefName), assemblyName);
+            return this.navToLocations((0, util_2.parseLocStrings)(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
         },
         /**
          * #action
@@ -1327,16 +1352,19 @@ function stateModelFactory(pluginManager) {
                 {
                     label: 'Zoom to region',
                     icon: ZoomIn_1.default,
-                    onClick: () => self.moveTo(self.leftOffset, self.rightOffset),
+                    onClick: () => {
+                        self.moveTo(self.leftOffset, self.rightOffset);
+                    },
                 },
                 {
                     label: 'Get sequence',
                     icon: MenuOpen_1.default,
-                    onClick: () => (0, util_1.getSession)(self).queueDialog(handleClose => [
-                        GetSequenceDialog,
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                        { model: self, handleClose },
-                    ]),
+                    onClick: () => {
+                        (0, util_1.getSession)(self).queueDialog(handleClose => [
+                            GetSequenceDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
                 },
             ];
         },
@@ -1410,6 +1438,7 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .preProcessSnapshot(snap => {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -23,7 +23,6 @@ async function renderToSvg(model, opts) {
     const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => children, } = opts;
     const session = (0, util_1.getSession)(model);
     const { allThemes } = session;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
     const theme = allThemes === null || allThemes === void 0 ? void 0 : allThemes()[themeName];
     const { width, tracks, showCytobands } = model;

package/dist/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -17,7 +17,7 @@ function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = tr
     return (react_1.default.createElement(react_1.default.Fragment, null,
         ticks.map(tick => {
             const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (react_1.default.createElement("line", { key: 'tick-' + tick.base, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }));
+            return (react_1.default.createElement("line", { key: `tick-${tick.base}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }));
         }),
         !hideText
             ? ticks

package/dist/LinearGenomeView/util.d.ts

@@ -20,7 +20,7 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
  *
  * Used by navToLocations and navToLocString
  */
-export declare function generateLocations(regions: ParsedLocString[] | undefined, assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+export declare function generateLocations(regions: ParsedLocString[], assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;

package/dist/LinearGenomeView/util.js

@@ -40,9 +40,6 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
     let minBase = start;
     let maxBase = end;
-    if (minBase === null || maxBase === null) {
-        return [];
-    }
     if (bpPerPx < 0) {
         ;
         [minBase, maxBase] = [maxBase, minBase];
@@ -73,7 +70,7 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
  *
  * Used by navToLocations and navToLocString
  */
-async function generateLocations(regions = [], assemblyManager, assemblyName) {
+async function generateLocations(regions, assemblyManager, assemblyName) {
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -129,15 +126,13 @@ function parseLocStrings(input, assemblyName, isValidRefName) {
         // if this fails, try interpreting as a whitespace-separated refname,
         // start, end if start and end are integer inputs
         const [refName, start, end] = inputs;
-        if (`${e}`.match(/Unknown reference sequence/) &&
+        if (/Unknown reference sequence/.exec(`${e}`) &&
             Number.isInteger(+start) &&
             Number.isInteger(+end)) {
             return [
-                (0, util_1.parseLocString)(refName + ':' + start + '..' + end, ref => isValidRefName(ref, assemblyName)),
+                (0, util_1.parseLocString)(`${refName}:${start}..${end}`, ref => isValidRefName(ref, assemblyName)),
             ];
         }
-        else {
-            throw e;
-        }
+        throw e;
     }
 }