@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/shared/SharedVariantMixin.js

@@ -0,0 +1,58 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SharedVariantMixin;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function SharedVariantMixin(configSchema) {
+    return mobx_state_tree_1.types
+        .compose(plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
+        selectedRendering: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
+        summaryScoreMode: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        rendererTypeNameState: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+    }))
+        .volatile(() => ({
+        message: undefined,
+    }))
+        .actions(self => ({
+        selectFeature(feature) {
+            const session = (0, util_1.getSession)(self);
+            if ((0, util_1.isSelectionContainer)(session)) {
+                session.setSelection(feature);
+            }
+        },
+        setRendererType(val) {
+            self.rendererTypeNameState = val;
+        },
+    }))
+        .views(self => ({
+        get adapterTypeName() {
+            return self.adapterConfig.type;
+        },
+        get rendererTypeNameSimple() {
+            var _a;
+            return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'defaultRendering');
+        },
+        get filters() {
+            return undefined;
+        },
+    }))
+        .views(self => ({
+        get adapterCapabilities() {
+            const type = self.adapterTypeName;
+            const { pluginManager } = (0, util_1.getEnv)(self);
+            return pluginManager.getAdapterType(type).adapterCapabilities;
+        },
+    }))
+        .actions(self => {
+        const { reload: superReload } = self;
+        return {
+            async reload() {
+                self.setError();
+                superReload();
+            },
+        };
+    });
+}

package/dist/shared/SourcesDataGrid.d.ts

@@ -0,0 +1,6 @@
+import type { Source } from '../types';
+export default function SourcesDataGrid({ rows, onChange, setSelected, }: {
+    rows: Source[];
+    onChange: (arg: Source[]) => void;
+    setSelected: (arg: string[]) => void;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/SourcesDataGrid.js

@@ -0,0 +1,68 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SourcesDataGrid;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const ColorPicker_1 = __importDefault(require("@jbrowse/core/ui/ColorPicker"));
+const util_1 = require("@jbrowse/core/util");
+const x_data_grid_1 = require("@mui/x-data-grid");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    cell: {
+        whiteSpace: 'nowrap',
+        overflow: 'hidden',
+        textOverflow: 'ellipsis',
+    },
+});
+function SourcesDataGrid({ rows, onChange, setSelected, }) {
+    const { classes } = useStyles();
+    const { id: _id, name: _name, label: _label, color: _color, baseUri: _baseUri, HP: _HP, ...rest } = rows[0];
+    const [currSort, setCurrSort] = (0, react_1.useState)({
+        idx: 0,
+        field: null,
+    });
+    return ((0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
+                setSelected(arg);
+            }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
+                {
+                    field: 'color',
+                    headerName: 'Color',
+                    renderCell: params => {
+                        const { value, id } = params;
+                        return ((0, jsx_runtime_1.jsx)(ColorPicker_1.default, { color: value || 'blue', onChange: c => {
+                                const elt = rows.find(f => f.name === id);
+                                if (elt) {
+                                    elt.color = c;
+                                }
+                                onChange([...rows]);
+                            } }));
+                    },
+                },
+                {
+                    field: 'label',
+                    headerName: 'Name',
+                    width: (0, util_1.measureGridWidth)(rows.map(r => r.label)),
+                },
+                ...Object.keys(rest).map(val => ({
+                    field: val,
+                    renderCell: ({ value }) => ((0, jsx_runtime_1.jsx)("div", { className: classes.cell, children: (0, jsx_runtime_1.jsx)(ui_1.SanitizedHTML, { html: (0, util_1.getStr)(value) }) })),
+                    width: (0, util_1.measureGridWidth)(rows.map(r => `${r[val]}`)),
+                })),
+            ], sortModel: [], onSortModelChange: args => {
+                const sort = args[0];
+                const idx = (currSort.idx + 1) % 2;
+                const field = sort.field || currSort.field;
+                setCurrSort({ idx, field });
+                onChange(field
+                    ? [...rows].sort((a, b) => {
+                        const aa = (0, util_1.getStr)(a[field]);
+                        const bb = (0, util_1.getStr)(b[field]);
+                        return idx === 1 ? aa.localeCompare(bb) : bb.localeCompare(aa);
+                    })
+                    : rows);
+            } }) }));
+}

package/dist/shared/SourcesGrid.d.ts

@@ -0,0 +1,7 @@
+import type { Source } from '../types';
+declare function SourcesGrid({ rows, onChange, showTips, }: {
+    rows: Source[];
+    onChange: (arg: Source[]) => void;
+    showTips: boolean;
+}): import("react/jsx-runtime").JSX.Element;
+export default SourcesGrid;

package/dist/shared/SourcesGrid.js

@@ -0,0 +1,14 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const SourcesDataGrid_1 = __importDefault(require("./SourcesDataGrid"));
+const SourcesGridHeader_1 = __importDefault(require("./SourcesGridHeader"));
+function SourcesGrid({ rows, onChange, showTips, }) {
+    const [selected, setSelected] = (0, react_1.useState)([]);
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(SourcesGridHeader_1.default, { selected: selected, rows: rows, showTips: showTips, onChange: onChange }), (0, jsx_runtime_1.jsx)(SourcesDataGrid_1.default, { rows: rows, onChange: onChange, setSelected: setSelected })] }));
+}
+exports.default = SourcesGrid;

package/dist/shared/SourcesGridHeader.d.ts

@@ -0,0 +1,7 @@
+import type { Source } from '../types';
+export default function SourcesGridHeader({ selected, onChange, rows, showTips, }: {
+    onChange: (arg: Source[]) => void;
+    rows: Source[];
+    selected: string[];
+    showTips: boolean;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/SourcesGridHeader.js

@@ -0,0 +1,41 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SourcesGridHeader;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ColorPicker_1 = require("@jbrowse/core/ui/ColorPicker");
+const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
+const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardArrowUp"));
+const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowDown"));
+const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
+const material_1 = require("@mui/material");
+const util_1 = require("./util");
+function SourcesGridHeader({ selected, onChange, rows, showTips, }) {
+    const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
+    const [widgetColor, setWidgetColor] = (0, react_1.useState)('blue');
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !selected.length, onClick: event => {
+                    setAnchorEl(event.currentTarget);
+                }, children: "Change color of selected items" }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
+                    onChange((0, util_1.moveUp)([...rows], selected));
+                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowUp_1.default, {}), showTips ? 'Move selected items up' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
+                    onChange((0, util_1.moveDown)([...rows], selected));
+                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowDown_1.default, {}), showTips ? 'Move selected items down' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
+                    onChange((0, util_1.moveUp)([...rows], selected, rows.length));
+                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowUp_1.default, {}), showTips ? 'Move selected items to top' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
+                    onChange((0, util_1.moveDown)([...rows], selected, rows.length));
+                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowDown_1.default, {}), showTips ? 'Move selected items to bottom' : null] }), (0, jsx_runtime_1.jsx)(ColorPicker_1.ColorPopover, { anchorEl: anchorEl, color: widgetColor, onChange: c => {
+                    setWidgetColor(c);
+                    selected.forEach(id => {
+                        const elt = rows.find(f => f.name === id);
+                        if (elt) {
+                            elt.color = c;
+                        }
+                    });
+                    onChange([...rows]);
+                }, onClose: () => {
+                    setAnchorEl(null);
+                } })] }));
+}

package/dist/shared/multiVariantColor.d.ts

@@ -0,0 +1,3 @@
+export declare function getColorAlleleCount(alleles: string[]): string;
+export declare function getColorPhased(alleles: string[], HP: number): string;
+export declare function getColorPhasedWithPhaseSet(alleles: string[], HP: number, PS: string): string;

package/dist/shared/multiVariantColor.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getColorAlleleCount = getColorAlleleCount;
+exports.getColorPhased = getColorPhased;
+exports.getColorPhasedWithPhaseSet = getColorPhasedWithPhaseSet;
+const colors_1 = require("@jbrowse/core/ui/colors");
+const colord_1 = require("@jbrowse/core/util/colord");
+const util_1 = require("../util");
+function getColorAlleleCount(alleles) {
+    const total = alleles.length;
+    let alt = 0;
+    let uncalled = 0;
+    let alt2 = 0;
+    let ref = 0;
+    for (const allele of alleles) {
+        if (allele === '1') {
+            alt++;
+        }
+        else if (allele === '0') {
+            ref++;
+        }
+        else if (allele === '.') {
+            uncalled++;
+        }
+        else {
+            alt2++;
+        }
+    }
+    if (ref === total) {
+        return `#ccc`;
+    }
+    else {
+        let a1 = (0, colord_1.colord)(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
+        if (alt2) {
+            a1 = a1.mix(`hsla(0,100%,20%,${alt2 / total})`);
+        }
+        if (uncalled) {
+            a1 = a1.mix(`hsla(50,50%,50%,${uncalled / total / 2})`);
+        }
+        return a1.toHex();
+    }
+}
+function getColorPhased(alleles, HP) {
+    const c = +alleles[HP];
+    return c ? colors_1.set1[c - 1] || 'black' : '#ccc';
+}
+function getColorPhasedWithPhaseSet(alleles, HP, PS) {
+    const c = +alleles[HP];
+    return c ? (0, util_1.colorify)(+PS) || 'black' : '#ccc';
+}

package/dist/shared/util.d.ts

@@ -0,0 +1,10 @@
+export declare function moveUp(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];
+export declare function moveDown(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];

package/dist/shared/util.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.moveUp = moveUp;
+exports.moveDown = moveDown;
+function moveUp(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => a - b);
+    let lastIdx = 0;
+    for (const old of idxs) {
+        const idx = Math.max(lastIdx, old - by);
+        if (idx >= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx + 1;
+    }
+    return arr;
+}
+function moveDown(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => b - a);
+    let lastIdx = arr.length - 1;
+    for (const old of idxs) {
+        const idx = Math.min(lastIdx, old + by);
+        if (idx <= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx - 1;
+    }
+    return arr;
+}

package/dist/types.d.ts

@@ -0,0 +1,14 @@
+export interface Source {
+    baseUri?: string;
+    name: string;
+    label?: string;
+    color?: string;
+    group?: string;
+    HP?: number;
+    id?: string;
+    [key: string]: unknown;
+}
+export interface SampleInfo {
+    isPhased: boolean;
+    maxPloidy: number;
+}

package/dist/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/util.d.ts

@@ -0,0 +1,8 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;
+export declare function getCol(gt: string): "blue" | "teal" | "#ccc" | "#CBC3E3";
+export declare function randomColor(str: string): string;
+export declare function colorify(n: number): string;
+export declare function findSecondLargest(arr: Iterable<number>): number;
+export declare function calculateMinorAlleleFrequency(feat: Feature): number;
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): Feature[];

package/dist/util.js

@@ -0,0 +1,86 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fillRectCtx = fillRectCtx;
+exports.getCol = getCol;
+exports.randomColor = randomColor;
+exports.colorify = colorify;
+exports.findSecondLargest = findSecondLargest;
+exports.calculateMinorAlleleFrequency = calculateMinorAlleleFrequency;
+exports.getFeaturesThatPassMinorAlleleFrequencyFilter = getFeaturesThatPassMinorAlleleFrequencyFilter;
+const util_1 = require("@jbrowse/core/util");
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+function getCol(gt) {
+    if (gt === '0|0' || gt === '0/0') {
+        return '#ccc';
+    }
+    else if (gt === '1|0' || gt === '0|1' || gt === '0/1' || gt === '1/0') {
+        return 'teal';
+    }
+    else if (gt === '1|1' || gt === '1/1') {
+        return 'blue';
+    }
+    else {
+        return '#CBC3E3';
+    }
+}
+function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
+    }
+    return `hsl(${colorify(sum * 10)}, 50%, 50%)`;
+}
+function colorify(n) {
+    return `hsl(${n % 255}, 50%, 50%)`;
+}
+function findSecondLargest(arr) {
+    let firstMax = 0;
+    let secondMax = 0;
+    for (const num of arr) {
+        if (num > firstMax) {
+            secondMax = firstMax;
+            firstMax = num;
+        }
+        else if (num > secondMax && num !== firstMax) {
+            secondMax = num;
+        }
+    }
+    return secondMax;
+}
+function calculateMinorAlleleFrequency(feat) {
+    if (feat.get('end') - feat.get('start') <= 10) {
+        const samp = feat.get('genotypes');
+        const alleleCounts = new Map();
+        for (const val of Object.values(samp)) {
+            const alleles = val.split(/[/|]/);
+            for (const allele of alleles) {
+                alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
+            }
+        }
+        return (findSecondLargest(alleleCounts.values()) /
+            ((0, util_1.sum)(alleleCounts.values()) || 1));
+    }
+    return -1;
+}
+function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+    const mafs = [];
+    for (const feat of feats) {
+        if (calculateMinorAlleleFrequency(feat) >= minorAlleleFrequencyFilter) {
+            mafs.push(feat);
+        }
+    }
+    return mafs;
+}

package/esm/ChordVariantDisplay/index.d.ts

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

package/esm/ChordVariantDisplay/index.js

@@ -1,6 +1,5 @@
-import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-// locals
+import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view';
 import configSchemaF from './models/configSchema';
 import stateModelF from './models/stateModelFactory';
 export default function ChordVariantDisplayF(pluginManager) {

package/esm/ChordVariantDisplay/models/configSchema.d.ts

@@ -1,8 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     renderer: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IAnyModelType, [undefined]>;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     onChordClick: {

package/esm/ChordVariantDisplay/models/configSchema.js

@@ -1,20 +1,11 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseChordDisplayConfig } from '@jbrowse/plugin-circular-view';
 import { types } from 'mobx-state-tree';
-/**
- * #config ChordVariantDisplay
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 function stateModelFactory(pluginManager) {
     return ConfigurationSchema('ChordVariantDisplay', {
-        /**
-         * #slot
-         */
         renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: baseChordDisplayConfig,
         explicitlyTyped: true,
     });

package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts

@@ -1,10 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
-/**
- * #stateModel ChordVariantDisplay
- * extends
- * - [BaseChordDisplay](../basechorddisplay)
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare const 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>;
@@ -21,13 +16,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"ChordVariantDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -98,36 +87,29 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
 } & {
     onChordClick(feature: Feature): void;
 } & {
-    readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
+    readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/slices").Slice[];
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType | undefined;
-    isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): renderer is import("@jbrowse/core/pluggableElementTypes").CircularChordRendererType;
     readonly selectedFeatureId: string | undefined;
 } & {
     renderStarted(): void;
     renderSuccess({ message, data, reactElement, html, renderingComponent, }: {
-        message: string;
-        data: any;
-        html: string;
-        reactElement: React.ReactElement;
-        renderingComponent: import("@jbrowse/core/util").AnyReactComponentType;
+        message?: string;
+        data?: any;
+        html?: string;
+        reactElement?: React.ReactElement;
+        renderingComponent?: import("@jbrowse/core/util").AnyReactComponentType;
     }): void;
     renderError(error: unknown): void;
     setRefNameMap(refNameMap: Record<string, string>): void;
 } & {
     afterAttach(): void;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/models/model").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/model").ExportSvgOptions & {
         theme?: import("@mui/material").ThemeOptions;
-    }): Promise<import("react").JSX.Element>;
+    }): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
-    /**
-     * #getter
-     */
     readonly rendererTypeName: any;
-    /**
-     * #method
-     */
     renderProps(): Record<string, unknown>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;

package/esm/ChordVariantDisplay/models/stateModelFactory.js

@@ -1,35 +1,18 @@
-import { BaseChordDisplayModel, } from '@jbrowse/plugin-circular-view';
-import { ConfigurationReference, } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { ConfigurationReference } from '@jbrowse/core/configuration';
 import { getContainingView } from '@jbrowse/core/util';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
-/**
- * #stateModel ChordVariantDisplay
- * extends
- * - [BaseChordDisplay](../basechorddisplay)
- */
+import { BaseChordDisplayModel } from '@jbrowse/plugin-circular-view';
+import { types } from 'mobx-state-tree';
 const stateModelFactory = (configSchema) => {
     return types
         .compose('ChordVariantDisplay', BaseChordDisplayModel, types.model({
-        /**
-         * #property
-         */
         type: types.literal('ChordVariantDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
-        /**
-         * #method
-         */
         renderProps() {
             const view = getContainingView(self);
             return {
@@ -47,8 +30,4 @@ const stateModelFactory = (configSchema) => {
         },
     }));
 };
-// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
-// render request is for 1.5x the current viewing window
-// tracks all have a height
-//
 export default stateModelFactory;

package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -1,5 +1,5 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{

package/esm/LinearVariantDisplay/configSchema.js

@@ -1,17 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
-/**
- * #config LinearVariantDisplay
- * mostly empty, this display type is very much
- * like a `FeatureTrack` with a `LinearBasicDisplay` except it has a custom
- * feature details widget
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 export default function configSchemaF(pluginManager) {
     return ConfigurationSchema('LinearVariantDisplay', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
         explicitlyTyped: true,
     });

package/esm/LinearVariantDisplay/index.d.ts

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

package/esm/LinearVariantDisplay/index.js

@@ -1,7 +1,7 @@
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import stateModelFactory from './model';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import configSchemaF from './configSchema';
+import stateModelFactory from './model';
 export default function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);