@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,15 +0,0 @@
-"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 plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const mobx_react_1 = require("mobx-react");
-const TooltipContents_1 = __importDefault(require("./TooltipContents"));
-const SNPCoverageTooltip = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureUnderMouse: feat } = model;
-    return feat && feat.get('type') === 'skip' ? null : ((0, jsx_runtime_1.jsx)(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents_1.default, ...props }));
-});
-exports.default = SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/TooltipContents.d.ts

@@ -1,11 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-interface Props {
-    feature: Feature;
-    model: {
-        visibleModifications: Map<string, {
-            color: string;
-        }>;
-    };
-}
-declare const TooltipContents: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
-export default TooltipContents;

package/dist/LinearSNPCoverageDisplay/components/TooltipContents.js

@@ -1,48 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
-    td: {
-        whiteSpace: 'nowrap',
-    },
-}));
-const toP = (s = 0) => +(+s).toFixed(1);
-const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-function ColorSquare({ base, model, }) {
-    var _a;
-    const { visibleModifications } = model;
-    return base.startsWith('mod_') ? ((0, jsx_runtime_1.jsx)("div", { style: {
-            width: 10,
-            height: 10,
-            background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
-        } })) : null;
-}
-const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2(props, reactRef) {
-    const { feature, model } = props;
-    const { classes } = useStyles();
-    const start = feature.get('start') + 1;
-    const end = feature.get('end');
-    const name = feature.get('refName');
-    const { refbase, readsCounted, depth, ref, ...info } = feature.get('snpinfo');
-    return ((0, jsx_runtime_1.jsx)("div", { ref: reactRef, children: (0, jsx_runtime_1.jsxs)("table", { children: [(0, jsx_runtime_1.jsx)("caption", { children: [
-                        name,
-                        start === end
-                            ? (0, util_1.toLocale)(start)
-                            : `${(0, util_1.toLocale)(start)}..${(0, util_1.toLocale)(end)}`,
-                    ]
-                        .filter(f => !!f)
-                        .join(':') }), (0, jsx_runtime_1.jsx)("thead", { children: (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("th", {}), (0, jsx_runtime_1.jsx)("th", { children: "Base" }), (0, jsx_runtime_1.jsx)("th", { children: "Count" }), (0, jsx_runtime_1.jsx)("th", { children: "% of Total" }), (0, jsx_runtime_1.jsx)("th", { children: "Strands" })] }) }), (0, jsx_runtime_1.jsxs)("tbody", { children: [(0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsx)("td", { children: "Total" }), (0, jsx_runtime_1.jsx)("td", { children: readsCounted }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }), (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsxs)("td", { children: ["REF ", refbase ? `(${refbase.toUpperCase()})` : ''] }), (0, jsx_runtime_1.jsx)("td", { children: ref.entryDepth }), (0, jsx_runtime_1.jsx)("td", { children: pct(ref.entryDepth, readsCounted) }), (0, jsx_runtime_1.jsxs)("td", { children: [ref['-1'] ? `${ref['-1']}(-)` : '', ref['1'] ? `${ref['1']}(+)` : ''] })] }), Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", { children: (0, jsx_runtime_1.jsx)(ColorSquare, { model: model, base: base }) }), (0, jsx_runtime_1.jsxs)("td", { children: [base.toUpperCase(), " "] }), (0, jsx_runtime_1.jsx)("td", { className: classes.td, children: [
-                                        score.entryDepth,
-                                        score.avgProbability !== undefined
-                                            ? `(avg. ${pct(score.avgProbability)} prob.)`
-                                            : '',
-                                    ]
-                                        .filter(f => !!f)
-                                        .join(' ') }), (0, jsx_runtime_1.jsx)("td", { children: base === 'depth' || base === 'skip'
-                                        ? '---'
-                                        : pct(score.entryDepth, readsCounted) }), (0, jsx_runtime_1.jsxs)("td", { children: [score['-1'] ? `${score['-1']}(-)` : '', score['1'] ? `${score['1']}(+)` : ''] })] }, `${key}_${base}`))))] })] }) }));
-});
-exports.default = TooltipContents;

package/dist/LinearSNPCoverageDisplay/configSchema.d.ts

@@ -1,80 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    scaleType: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    inverted: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    multiTicks: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    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;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearSNPCoverageDisplay/configSchema.js

@@ -1,62 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SNPCoverageConfigFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("../shared/util");
-function x() { }
-function SNPCoverageConfigFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: mobx_state_tree_1.types.enumeration('Autoscale type', ['local']),
-            description: 'performs local autoscaling (no other options for SNP Coverage available)',
-        },
-        minScore: {
-            type: 'number',
-            defaultValue: Number.MIN_VALUE,
-            description: 'minimum value for the y-scale',
-        },
-        maxScore: {
-            type: 'number',
-            description: 'maximum value for the y-scale',
-            defaultValue: Number.MAX_VALUE,
-        },
-        scaleType: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
-            description: 'The type of scale to use',
-            defaultValue: 'linear',
-        },
-        inverted: {
-            type: 'boolean',
-            description: 'draw upside down',
-            defaultValue: false,
-        },
-        multiTicks: {
-            type: 'boolean',
-            description: 'Display multiple values for the ticks',
-            defaultValue: false,
-        },
-        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
-            SNPCoverageRenderer: pluginManager.getRendererType('SNPCoverageRenderer').configSchema,
-        }),
-        colorBy: {
-            type: 'frozen',
-            description: 'color scheme to use',
-            defaultValue: {
-                type: 'normal',
-            },
-        },
-        filterBy: {
-            type: 'frozen',
-            description: 'default filters to use',
-            defaultValue: util_1.defaultFilterFlags,
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}

package/dist/LinearSNPCoverageDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;

package/dist/LinearSNPCoverageDisplay/index.js

@@ -1,24 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = register;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function register(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearSNPCoverageDisplay',
-            displayName: 'SNPCoverage display',
-            configSchema,
-            stateModel: (0, model_1.default)(pluginManager, configSchema),
-            trackType: 'AlignmentsTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: plugin_wiggle_1.LinearWiggleDisplayReactComponent,
-        });
-    });
-}

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -1,111 +0,0 @@
-import type { ColorBy, FilterBy } from '../shared/types';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-declare function stateModelFactory(pluginManager: PluginManager, 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>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        stopToken: string | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: {
-                error?: unknown;
-                reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
-                reactElement?: React.ReactElement;
-            };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
-        setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        maxFeatureScreenDensity: {
-            type: string;
-            description: string;
-            defaultValue: number;
-        };
-        fetchSizeLimit: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        height: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        mouseover: {
-            type: string;
-            description: string;
-            defaultValue: string;
-            contextVariable: string[];
-        };
-        jexlFilters: {
-            type: string;
-            description: string;
-            defaultValue: never[];
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
-} & {
-    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    configuration: AnyConfigurationSchemaType;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-    invertedSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    showInterbaseIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    showArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-}, never, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
-export default stateModelFactory;

package/dist/LinearSNPCoverageDisplay/model.js

@@ -1,262 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-const util_1 = require("@jbrowse/core/util");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const getUniqueModifications_1 = require("../shared/getUniqueModifications");
-const util_2 = require("../util");
-const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
-const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-function stateModelFactory(pluginManager, configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-        showInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        showInterbaseIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        showArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        filterBySetting: mobx_state_tree_1.types.frozen(),
-        colorBySetting: mobx_state_tree_1.types.frozen(),
-        jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
-    }))
-        .volatile(() => ({
-        visibleModifications: mobx_1.observable.map({}),
-        modificationsReady: false,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-    }))
-        .actions(self => ({
-        setConfig(configuration) {
-            self.configuration = configuration;
-        },
-        setFilterBy(filter) {
-            self.filterBySetting = {
-                ...filter,
-            };
-        },
-        setColorScheme(colorBy) {
-            self.colorBySetting = colorBy
-                ? {
-                    ...colorBy,
-                }
-                : undefined;
-        },
-        setJexlFilters(filters) {
-            self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
-        },
-        updateVisibleModifications(uniqueModifications) {
-            for (const modification of uniqueModifications) {
-                if (!self.visibleModifications.has(modification.type)) {
-                    self.visibleModifications.set(modification.type, {
-                        ...modification,
-                        color: (0, util_2.getColorForModification)(modification.type),
-                    });
-                }
-            }
-        },
-    }))
-        .views(self => {
-        const { adapterProps: superAdapterProps } = self;
-        return {
-            get rendererConfig() {
-                const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-                const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
-                return self.rendererType.configSchema.create({
-                    ...configBlob,
-                    showInterbaseCounts: showInterbaseCounts !== null && showInterbaseCounts !== void 0 ? showInterbaseCounts : configBlob.showInterbaseCounts,
-                    showInterbaseIndicators: showInterbaseIndicators !== null && showInterbaseIndicators !== void 0 ? showInterbaseIndicators : configBlob.showInterbaseIndicators,
-                    showArcs: showArcs !== null && showArcs !== void 0 ? showArcs : configBlob.showArcs,
-                }, (0, mobx_state_tree_1.getEnv)(self));
-            },
-            get showArcsSetting() {
-                var _a;
-                return ((_a = self.showArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showArcs'));
-            },
-            get showInterbaseCountsSetting() {
-                var _a;
-                return ((_a = self.showInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseCounts'));
-            },
-            get showInterbaseIndicatorsSetting() {
-                var _a;
-                return ((_a = self.showInterbaseIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseIndicators'));
-            },
-            get autorunReady() {
-                const view = (0, util_1.getContainingView)(self);
-                return (view.initialized &&
-                    self.statsReadyAndRegionNotTooLarge &&
-                    !self.error);
-            },
-            adapterProps() {
-                const superProps = superAdapterProps();
-                const { filters, filterBy } = self;
-                return {
-                    ...superProps,
-                    filters,
-                    filterBy,
-                };
-            },
-        };
-    })
-        .actions(self => ({
-        setModificationsReady(flag) {
-            self.modificationsReady = flag;
-        },
-        setShowInterbaseIndicators(arg) {
-            self.showInterbaseIndicators = arg;
-        },
-        setShowInterbaseCounts(arg) {
-            self.showInterbaseCounts = arg;
-        },
-        setShowArcs(arg) {
-            self.showArcs = arg;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, util_2.createAutorun)(self, async () => {
-                self.setModificationsReady(false);
-                if (!self.autorunReady) {
-                    return;
-                }
-                const view = (0, util_1.getContainingView)(self);
-                const { staticBlocks } = view;
-                const { colorBy } = self;
-                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                    const vals = await (0, getUniqueModifications_1.getUniqueModifications)({
-                        model: self,
-                        adapterConfig: (0, configuration_1.getConf)(self.parentTrack, 'adapter'),
-                        blocks: staticBlocks,
-                    });
-                    if ((0, mobx_state_tree_1.isAlive)(self)) {
-                        self.updateVisibleModifications(vals);
-                        self.setModificationsReady(true);
-                    }
-                }
-                else {
-                    self.setModificationsReady(true);
-                }
-            }, { delay: 1000 });
-        },
-    }))
-        .views(self => {
-        const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
-        return {
-            renderReady() {
-                const superProps = superRenderProps();
-                return !superProps.notReady && self.modificationsReady;
-            },
-            renderProps() {
-                const { colorBy, visibleModifications } = self;
-                return {
-                    ...superRenderProps(),
-                    notReady: !this.renderReady(),
-                    colorBy,
-                    visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
-                };
-            },
-            get TooltipComponent() {
-                return Tooltip;
-            },
-            get adapterConfig() {
-                const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-                return {
-                    type: 'SNPCoverageAdapter',
-                    subadapter,
-                };
-            },
-            get rendererTypeName() {
-                return rendererTypes.get('snpcoverage');
-            },
-            get graphType() {
-                return true;
-            },
-            contextMenuItems() {
-                return [];
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Show insertion/clipping indicators',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showInterbaseIndicatorsSetting,
-                        onClick: () => {
-                            self.setShowInterbaseIndicators(!self.showInterbaseIndicatorsSetting);
-                        },
-                    },
-                    {
-                        label: 'Show insertion/clipping counts',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showInterbaseCountsSetting,
-                        onClick: () => {
-                            self.setShowInterbaseCounts(!self.showInterbaseCountsSetting);
-                        },
-                    },
-                    {
-                        label: 'Show arcs',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showArcsSetting,
-                        onClick: () => {
-                            self.setShowArcs(!self.showArcsSetting);
-                        },
-                    },
-                ];
-            },
-            get filters() {
-                return new serializableFilterChain_1.default({ filters: self.jexlFilters });
-            },
-        };
-    });
-}
-exports.default = stateModelFactory;

package/dist/MismatchParser/cigarToMismatches.d.ts

@@ -1,2 +0,0 @@
-import type { Mismatch } from '../shared/types';
-export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];

package/dist/MismatchParser/getNextRefPos.d.ts

@@ -1,4 +0,0 @@
-export declare function getNextRefPos(cigarOps: string[], positions: number[]): {
-    ref: number;
-    idx: number;
-}[];