@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/LinearReadCloudDisplay/configSchema.js

@@ -1,46 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
-import { types } from 'mobx-state-tree';
-/**
- * #config LinearReadCloudDisplay
- */
 function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearReadCloudDisplay', {
-        /**
-         * #slot
-         */
         maxFeatureScreenDensity: {
             type: 'number',
             description: 'maximum features per pixel that is displayed in the view',
             defaultValue: 5,
         },
-        /**
-         * #slot
-         */
         featureHeight: {
             type: 'number',
             defaultValue: 7,
         },
-        /**
-         * #slot
-         */
-        colorScheme: {
-            type: 'stringEnum',
-            model: types.enumeration('colorScheme', [
-                'strand',
-                'normal',
-                'insertSize',
-                'insertSizeAndOrientation',
-                'mappingQuality',
-                'tag',
-            ]),
-            description: 'color scheme to use',
-            defaultValue: 'normal',
+        colorBy: {
+            type: 'frozen',
+            defaultValue: { type: 'insertSizeAndOrientation' },
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearReadCloudDisplay/drawFeats.d.ts

@@ -1,2 +1,2 @@
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
 export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -1,7 +1,7 @@
 import { getContainingView, getSession } from '@jbrowse/core/util';
-import { hasPairedReads } from '../shared/util';
-import { drawPairChains } from './drawPairChains';
 import { drawLongReadChains } from './drawLongReadChains';
+import { drawPairChains } from './drawPairChains';
+import { hasPairedReads } from '../shared/util';
 export function drawFeats(self, ctx) {
     const { chainData } = self;
     if (!chainData) {

package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -1,7 +1,7 @@
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ChainData } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -1,7 +1,7 @@
 import { getConf } from '@jbrowse/core/configuration';
 import { max, min } from '@jbrowse/core/util';
-import { fillColor, strokeColor } from '../shared/color';
 import { fillRectCtx, strokeRectCtx } from './util';
+import { fillColor, strokeColor } from '../shared/color';
 export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     var _a, _b, _c, _d, _e;
     const distances = [];
@@ -9,8 +9,6 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const { chains } = chainData;
     const { height } = self;
     const featureHeight = getConf(self, 'featureHeight');
-    // get bounds on the 'distances' (pixel span that a particular split long
-    // read 'chain' would have in view)
     for (const chain of chains) {
         let minX = Number.MAX_VALUE;
         let maxX = Number.MIN_VALUE;
@@ -31,7 +29,6 @@ export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
     const minD = Math.max(Math.log(min(distances)) - 1, 0);
     const scaler = (height - 20) / (maxD - minD);
     const halfHeight = featureHeight / 2 - 0.5;
-    // draw split long read 'chains' as connected entities
     for (let i = 0; i < chains.length; i++) {
         const chain = chains[i];
         const w = distances[i];

package/esm/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -1,7 +1,7 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
-import { LinearReadCloudDisplayModel } from './model';
+import type { LinearReadCloudDisplayModel } from './model';
+import type { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
     ctx: CanvasRenderingContext2D;
     self: LinearReadCloudDisplayModel;

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -9,9 +9,6 @@ export function drawPairChains({ ctx, self, chainData, view, asm, }) {
     const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
     const { chains, stats } = chainData;
     for (const chain of chains) {
-        // if we're looking at a paired read (flag 1) then assume it is just
-        // two reads (some small cases may defy this assumption such as
-        // secondary alignments but this may be uncommon)
         if (chain.length > 1) {
             const v0 = chain[0];
             const v1 = chain[1];

package/esm/LinearReadCloudDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;

package/esm/LinearReadCloudDisplay/index.js

@@ -1,8 +1,7 @@
+import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-// locals
 import configSchemaF from './configSchema';
 import stateModelF from './model';
-import { lazy } from 'react';
 export default function register(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -1,16 +1,8 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ColorBy, FilterBy } from '../shared/types';
-import { ChainData } from '../shared/fetchChains';
-/**
- * #stateModel LinearReadCloudDisplay
- * it is not a block based track, hence not BaseLinearDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import type React from 'react';
+import type { ChainData } from '../shared/fetchChains';
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -23,8 +15,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
     configuration: AnyConfigurationSchemaType;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
@@ -62,20 +54,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import(
-            /**
-             * #action
-             */
-            "mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -121,8 +107,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
     chainData: ChainData | undefined;
@@ -130,50 +117,24 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
 } & {
-    /**
-     * #action
-     */
+    readonly colorBy: any;
+    readonly filterBy: any;
+} & {
     setDrawSingletons(f: boolean): void;
-    /**
-     * #action
-     */
     setLastDrawnOffsetPx(n: number): void;
-    /**
-     * #action
-     */
     setLastDrawnBpPerPx(n: number): void;
-    /**
-     * #action
-     */
     setLoading(f: boolean): void;
-    /**
-     * #action
-     */
     reload(): void;
-    /**
-     * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw
-     * the canvas
-     */
     setRef(ref: HTMLCanvasElement | null): void;
     setColorScheme(colorBy: {
         type: string;
     }): void;
-    /**
-     * #action
-     */
     setChainData(args: ChainData): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
 } & {
     readonly drawn: boolean;
 } & {
     renderProps(): any;
-    /**
-     * #method
-     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         type: string;
@@ -203,9 +164,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         checked?: undefined;
         onClick?: undefined;
     })[];
-    /**
-     * #method
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/esm/LinearReadCloudDisplay/model.js

@@ -1,45 +1,19 @@
 import { lazy } from 'react';
-import { types } from 'mobx-state-tree';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
-import { ConfigurationReference, } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { FeatureDensityMixin, TrackHeightMixin, } from '@jbrowse/plugin-linear-genome-view';
-// icons
-import PaletteIcon from '@mui/icons-material/Palette';
 import FilterListIcon from '@mui/icons-material/ClearAll';
-import { defaultFilterFlags } from '../shared/util';
-// async
+import PaletteIcon from '@mui/icons-material/Palette';
+import { types } from 'mobx-state-tree';
 const FilterByTagDialog = lazy(() => import('../shared/components/FilterByTagDialog'));
-/**
- * #stateModel LinearReadCloudDisplay
- * it is not a block based track, hence not BaseLinearDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
 function stateModelFactory(configSchema) {
     return types
         .compose('LinearReadCloudDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearReadCloudDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        filterBy: types.optional(types.frozen(), defaultFilterFlags),
-        /**
-         * #property
-         */
-        colorBy: types.frozen(),
-        /**
-         * #property
-         */
+        filterBySetting: types.frozen(),
+        colorBySetting: types.frozen(),
         drawSingletons: true,
     }))
         .volatile(() => ({
@@ -48,62 +22,46 @@ function stateModelFactory(configSchema) {
         lastDrawnOffsetPx: undefined,
         lastDrawnBpPerPx: 0,
         ref: null,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setDrawSingletons(f) {
             self.drawSingletons = f;
         },
-        /**
-         * #action
-         */
         setLastDrawnOffsetPx(n) {
             self.lastDrawnOffsetPx = n;
         },
-        /**
-         * #action
-         */
         setLastDrawnBpPerPx(n) {
             self.lastDrawnBpPerPx = n;
         },
-        /**
-         * #action
-         */
         setLoading(f) {
             self.loading = f;
         },
-        /**
-         * #action
-         */
         reload() {
             self.error = undefined;
         },
-        /**
-         * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw
-         * the canvas
-         */
         setRef(ref) {
             self.ref = ref;
         },
         setColorScheme(colorBy) {
-            self.colorBy = {
+            self.colorBySetting = {
                 ...colorBy,
             };
         },
-        /**
-         * #action
-         */
         setChainData(args) {
             self.chainData = args;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
@@ -116,17 +74,12 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            // we don't use a server side renderer, so this fills in minimal
-            // info so as not to crash
             renderProps() {
                 return {
                     ...superRenderProps(),
                     notReady: !self.chainData,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -180,9 +133,6 @@ function stateModelFactory(configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             */
             async renderSvg(opts) {
                 const { renderSvg } = await import('../shared/renderSvgUtil');
                 const { drawFeats } = await import('./drawFeats');
@@ -192,7 +142,6 @@ function stateModelFactory(configSchema) {
     })
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {

package/esm/LinearReadCloudDisplay/util.js

@@ -1,4 +1,3 @@
-// avoid drawing negative width features for SVG exports
 export function fillRectCtx(x, y, width, height, ctx, fillColor) {
     if (width < 0) {
         x += width;

package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
     model: {
@@ -9,5 +8,5 @@ declare const SNPCoverageTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default SNPCoverageTooltip;

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,7 +1,8 @@
-import React from 'react';
-import { observer } from 'mobx-react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { forwardRef } from 'react';
 import { toLocale } from '@jbrowse/core/util';
 import { Tooltip } from '@jbrowse/plugin-wiggle';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(() => ({
     td: {
@@ -10,7 +11,7 @@ const useStyles = makeStyles()(() => ({
 }));
 const toP = (s = 0) => +(+s).toFixed(1);
 const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-const TooltipContents = React.forwardRef(function TooltipContents2(props, reactRef) {
+const TooltipContents = forwardRef(function TooltipContents2(props, reactRef) {
     const { feature, model } = props;
     const { classes } = useStyles();
     const start = feature.get('start') + 1;
@@ -23,58 +24,21 @@ const TooltipContents = React.forwardRef(function TooltipContents2(props, reactR
     ]
         .filter(f => !!f)
         .join(':');
-    return (React.createElement("div", { ref: reactRef },
-        React.createElement("table", null,
-            React.createElement("caption", null, loc),
-            React.createElement("thead", null,
-                React.createElement("tr", null,
-                    React.createElement("th", null),
-                    React.createElement("th", null, "Base"),
-                    React.createElement("th", null, "Count"),
-                    React.createElement("th", null, "% of Total"),
-                    React.createElement("th", null, "Strands"))),
-            React.createElement("tbody", null,
-                React.createElement("tr", null,
-                    React.createElement("td", null),
-                    React.createElement("td", null, "Total"),
-                    React.createElement("td", null, readsCounted),
-                    React.createElement("td", null, " "),
-                    React.createElement("td", null, " ")),
-                React.createElement("tr", null,
-                    React.createElement("td", null),
-                    React.createElement("td", null,
-                        "REF ",
-                        refbase ? `(${refbase.toUpperCase()})` : ''),
-                    React.createElement("td", null, ref.entryDepth),
-                    React.createElement("td", null, pct(ref.entryDepth, readsCounted)),
-                    React.createElement("td", null,
-                        ref['-1'] ? `${ref['-1']}(-)` : '',
-                        ref['1'] ? `${ref['1']}(+)` : '')),
-                Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (React.createElement("tr", { key: `${key}_${base}` },
-                    React.createElement("td", null,
-                        React.createElement(ColorSquare, { model: model, base: base })),
-                    React.createElement("td", null,
-                        base.toUpperCase(),
-                        " "),
-                    React.createElement("td", { className: classes.td }, [
-                        score.entryDepth,
-                        score.avgProbability !== undefined
-                            ? `(avg. ${pct(score.avgProbability)} prob.)`
-                            : '',
-                    ]
-                        .filter(f => !!f)
-                        .join(' ')),
-                    React.createElement("td", null, base === 'depth' || base === 'skip'
-                        ? '---'
-                        : pct(score.entryDepth, readsCounted)),
-                    React.createElement("td", null,
-                        score['-1'] ? `${score['-1']}(-)` : '',
-                        score['1'] ? `${score['1']}(+)` : '')))))))));
+    return (_jsx("div", { ref: reactRef, children: _jsxs("table", { children: [_jsx("caption", { children: loc }), _jsx("thead", { children: _jsxs("tr", { children: [_jsx("th", {}), _jsx("th", { children: "Base" }), _jsx("th", { children: "Count" }), _jsx("th", { children: "% of Total" }), _jsx("th", { children: "Strands" })] }) }), _jsxs("tbody", { children: [_jsxs("tr", { children: [_jsx("td", {}), _jsx("td", { children: "Total" }), _jsx("td", { children: readsCounted }), _jsx("td", { children: " " }), _jsx("td", { children: " " })] }), _jsxs("tr", { children: [_jsx("td", {}), _jsxs("td", { children: ["REF ", refbase ? `(${refbase.toUpperCase()})` : ''] }), _jsx("td", { children: ref.entryDepth }), _jsx("td", { children: pct(ref.entryDepth, readsCounted) }), _jsxs("td", { children: [ref['-1'] ? `${ref['-1']}(-)` : '', ref['1'] ? `${ref['1']}(+)` : ''] })] }), Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (_jsxs("tr", { children: [_jsx("td", { children: _jsx(ColorSquare, { model: model, base: base }) }), _jsxs("td", { children: [base.toUpperCase(), " "] }), _jsx("td", { className: classes.td, children: [
+                                        score.entryDepth,
+                                        score.avgProbability !== undefined
+                                            ? `(avg. ${pct(score.avgProbability)} prob.)`
+                                            : '',
+                                    ]
+                                        .filter(f => !!f)
+                                        .join(' ') }), _jsx("td", { children: base === 'depth' || base === 'skip'
+                                        ? '---'
+                                        : pct(score.entryDepth, readsCounted) }), _jsxs("td", { children: [score['-1'] ? `${score['-1']}(-)` : '', score['1'] ? `${score['1']}(+)` : ''] })] }, `${key}_${base}`))))] })] }) }));
 });
 function ColorSquare({ base, model, }) {
     var _a;
     const { visibleModifications } = model;
-    return base.startsWith('mod_') ? (React.createElement("div", { style: {
+    return base.startsWith('mod_') ? (_jsx("div", { style: {
             width: 10,
             height: 10,
             background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
@@ -83,6 +47,6 @@ function ColorSquare({ base, model, }) {
 const SNPCoverageTooltip = observer(function (props) {
     const { model } = props;
     const { featureUnderMouse: feat } = model;
-    return feat && feat.get('type') === 'skip' ? null : (React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props }));
+    return feat && feat.get('type') === 'skip' ? null : (_jsx(Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 export default SNPCoverageTooltip;

package/esm/LinearSNPCoverageDisplay/configSchema.d.ts

@@ -1,60 +1,55 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     autoscale: {
         type: string;
         defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */ inverted: {
+    inverted: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     multiTicks: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    colorBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;