npm - @jbrowse/plugin-wiggle - Versions diffs - 2.4.0 → 2.4.2 - Mend

@jbrowse/plugin-wiggle 2.4.0 → 2.4.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (151) hide show

package/esm/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -41,9 +41,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
@@ -64,7 +62,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+     * #property
+     */
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
@@ -189,14 +189,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     reload(): void;
 } & {
     currBpPerPx: number;
-    scrollTop: number;
+    scrollTop: number; /**
+     * #property
+     */
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -207,7 +209,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -217,46 +219,39 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionsStatsP(arg: any): void;
+    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionsStats(): void;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void; /**
-     * #method
+    /**
+     * #getter
      */
+    reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -533,9 +528,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
@@ -556,7 +549,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+     * #property
+     */
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {

package/esm/LinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -174,12 +174,7 @@ function stateModelFactory(pluginManager, configSchema) {
          * #action
          */
         toggleLogScale() {
-            if (self.scale !== 'log') {
-                self.scale = 'log';
-            }
-            else {
-                self.scale = 'linear';
-            }
+            self.scale = self.scale === 'log' ? 'linear' : 'log';
         },
         /**
          * #action

package/esm/LinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiDensityRenderer/MultiDensityRenderer.js CHANGED Viewed

@@ -2,7 +2,7 @@ import { groupBy } from '../util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { drawDensity } from '../drawxy';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
-    // @ts-ignore
+    // @ts-expect-error
     async draw(ctx, props) {
         const { bpPerPx, sources, regions, features } = props;
         const [region] = regions;
@@ -27,7 +27,7 @@ export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
             ctx.lineTo(width, height);
             ctx.stroke();
             ctx.translate(0, height);
-            feats = feats.concat(reducedFeatures);
+            feats = [...feats, ...reducedFeatures];
         });
         ctx.restore();
         return { reducedFeatures: feats };

package/esm/MultiDensityRenderer/MultiDensityRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiLineRenderer/MultiLineRenderer.js CHANGED Viewed

@@ -2,7 +2,7 @@ import { drawLine } from '../drawxy';
 import { groupBy } from '../util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiLineRenderer extends WiggleBaseRenderer {
-    // @ts-ignore
+    // @ts-expect-error
     async draw(ctx, props) {
         const { sources, features } = props;
         const groups = groupBy([...features.values()], f => f.get('source'));
@@ -17,7 +17,7 @@ export default class MultiLineRenderer extends WiggleBaseRenderer {
                 features,
                 colorCallback: () => source.color || 'blue',
             });
-            feats = feats.concat(reducedFeatures);
+            feats = [...feats, ...reducedFeatures];
         });
         return { reducedFeatures: feats };
     }

package/esm/MultiLineRenderer/MultiLineRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js CHANGED Viewed

@@ -27,7 +27,7 @@ function DraggableDialog(props) {
             React.createElement(DialogTitle, { style: { cursor: 'move' }, id: "draggable-dialog-title" },
                 title,
                 onClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => {
-                        // @ts-ignore
+                        // @ts-expect-error
                         onClose();
                     } },
                     React.createElement(CloseIcon, null))) : null),

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js CHANGED Viewed

@@ -56,7 +56,7 @@ export default function SetColorDialog({ model, handleClose, }) {
 function SourcesGrid({ rows, onChange, showTips, }) {
     const [anchorEl, setAnchorEl] = useState(null);
     const [selected, setSelected] = useState([]);
-    // @ts-ignore
+    // @ts-expect-error
     const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
     // similar to BaseFeatureDetail data-grid for auto-measuring columns
     const columns = [
@@ -87,7 +87,7 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                 const { value } = params;
                 return isUriLocation(value) ? React.createElement(UriLink, { value: value }) : getStr(value);
             },
-            // @ts-ignore
+            // @ts-expect-error
             width: measureGridWidth(rows.map(r => r[val])),
         })),
     ];
@@ -129,9 +129,9 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     setCurrSort({ idx, field });
                     onChange(field
                         ? [...rows].sort((a, b) => {
-                            // @ts-ignore
+                            // @ts-expect-error
                             const aa = getStr(a[field]);
-                            // @ts-ignore
+                            // @ts-expect-error
                             const bb = getStr(b[field]);
                             return idx === 1
                                 ? aa.localeCompare(bb)

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import { Source } from '../../util';
-import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
+import { TooltipContentsComponent } from '../../Tooltip';
 declare const TooltipContents: React.ForwardRefExoticComponent<{
     model: {
         sources: Source[];
@@ -22,4 +22,4 @@ declare const WiggleTooltip: (props: {
     TooltipContents?: TooltipContentsComponent;
 }) => JSX.Element;
 export default WiggleTooltip;
-export { Tooltip };
+export { default as Tooltip } from '../../Tooltip';

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js CHANGED Viewed

@@ -39,5 +39,5 @@ const WiggleTooltip = observer((props) => {
     return React.createElement(Tooltip, { useClientY: true, TooltipContents: TooltipContents, ...props });
 });
 export default WiggleTooltip;
-export { Tooltip };
+export { default as Tooltip } from '../../Tooltip';
 //# sourceMappingURL=Tooltip.js.map

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts CHANGED Viewed

@@ -1,6 +1,5 @@
 /// <reference types="react" />
 import { WiggleDisplayModel } from '../models/model';
-import YScaleBar from '../../shared/YScaleBar';
 export declare const StatBars: (props: {
     model: WiggleDisplayModel;
     orientation?: string;
@@ -10,4 +9,4 @@ declare const _default: (props: {
     model: WiggleDisplayModel;
 }) => JSX.Element;
 export default _default;
-export { YScaleBar };
+export { default as YScaleBar } from '../../shared/YScaleBar';

package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js CHANGED Viewed

@@ -59,8 +59,8 @@ const ColorLegend = observer(function ({ model, rowHeight, labelWidth, exportSVG
         needsFullHeightScalebar ? (React.createElement(RectBg, { y: 0, x: extraOffset, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null,
         sources.map((source, idx) => {
             const boxHeight = Math.min(20, rowHeight);
-            return (React.createElement(React.Fragment, { key: source.name + '-' + idx },
-                !needsFullHeightScalebar ? (React.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })) : null,
+            return (React.createElement(React.Fragment, { key: `${source.name}-${idx}` },
+                needsFullHeightScalebar ? null : (React.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })),
                 source.color ? (React.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: colorBoxWidth, height: needsCustomLegend ? rowHeight : boxHeight, color: source.color })) : null,
                 canDisplayLabel ? (React.createElement("text", { y: idx * rowHeight + 13, x: extraOffset + colorBoxWidth + 2, fontSize: svgFontSize }, source.name)) : null));
         }))) : null;
@@ -85,7 +85,7 @@ export const StatBars = observer(function (props) {
         React.createElement("g", { transform: `translate(${viewWidth - labelWidth - 100},0)` },
             React.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: 12, labelWidth: labelWidth })))) : (React.createElement(React.Fragment, null,
         React.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: model.rowHeight, labelWidth: labelWidth }),
-        rowHeightTooSmallForScalebar || needsCustomLegend ? (React.createElement(ScoreLegend, { ...props })) : (sources.map((_source, idx) => (React.createElement("g", { transform: `translate(0 ${rowHeight * idx})`, key: JSON.stringify(ticks) + '-' + idx },
+        rowHeightTooSmallForScalebar || needsCustomLegend ? (React.createElement(ScoreLegend, { ...props })) : (sources.map((_source, idx) => (React.createElement("g", { transform: `translate(0 ${rowHeight * idx})`, key: `${JSON.stringify(ticks)}-${idx}` },
             React.createElement(YScaleBar, { model: model, orientation: orientation })))))))));
 });
 export default observer((props) => {
@@ -94,5 +94,5 @@ export default observer((props) => {
         React.createElement(BaseLinearDisplayComponent, { ...props }),
         React.createElement(StatBars, { model: model })));
 });
-export { YScaleBar };
+export { default as YScaleBar } from '../../shared/YScaleBar';
 //# sourceMappingURL=WiggleDisplayComponent.js.map

package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/esm/MultiLinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -140,10 +140,10 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -154,7 +154,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
     readonly currentBytesRequested: number;
@@ -164,19 +164,16 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
-    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
-        headers?: Record<string, string> | undefined;
-        signal?: AbortSignal | undefined;
-        filters?: string[] | undefined;
-    }): Promise<{}>;
-    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
-    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionsStatsP(arg: any): void;
+    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionsStats(): void;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
@@ -190,18 +187,13 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -288,7 +280,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     };
     readonly autoscaleType: string;
     readonly displayCrossHatchesSetting: boolean;
-    readonly rowHeight: any;
+    readonly rowHeight: number;
     readonly rowHeightTooSmallForScalebar: boolean;
     readonly useMinimalTicks: any;
 } & {

package/esm/MultiLinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -124,12 +124,7 @@ const stateModelFactory = (pluginManager, configSchema) => types
         }
     },
     toggleLogScale() {
-        if (self.scale !== 'log') {
-            self.scale = 'log';
-        }
-        else {
-            self.scale = 'linear';
-        }
+        self.scale = self.scale === 'log' ? 'linear' : 'log';
     },
     setScaleType(scale) {
         self.scale = scale;