@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/shared/MultiVariantBaseModel.js

@@ -1,373 +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 });
-exports.default = MultiVariantBaseModelF;
-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 stopToken_1 = require("@jbrowse/core/util/stopToken");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const Category_1 = __importDefault(require("@mui/icons-material/Category"));
-const FilterList_1 = __importDefault(require("@mui/icons-material/FilterList"));
-const Height_1 = __importDefault(require("@mui/icons-material/Height"));
-const Splitscreen_1 = __importDefault(require("@mui/icons-material/Splitscreen"));
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const getSources_1 = require("./getSources");
-const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
-const MAFFilterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/MAFFilterDialog'))));
-const AddFiltersDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddFiltersDialog'))));
-const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/MultiVariantClusterDialog/ClusterDialog'))));
-const SetRowHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetRowHeightDialog'))));
-function MultiVariantBaseModelF(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearVariantMatrixDisplay', (0, plugin_linear_genome_view_1.linearBareDisplayStateModelFactory)(configSchema), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearVariantMatrixDisplay'),
-        layout: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        minorAlleleFrequencyFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-        showSidebarLabelsSetting: true,
-        renderingMode: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, 'alleleCount'),
-        rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 8),
-        autoHeight: true,
-        lengthCutoffFilter: Number.MAX_SAFE_INTEGER,
-        jexlFilters: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string)),
-        referenceDrawingMode: 'skip',
-    }))
-        .volatile(() => ({
-        sourcesLoadingStopToken: undefined,
-        simplifiedFeaturesStopToken: undefined,
-        featureUnderMouseVolatile: undefined,
-        sourcesVolatile: undefined,
-        featuresVolatile: undefined,
-        hasPhased: false,
-        sampleInfo: undefined,
-        hoveredGenotype: undefined,
-    }))
-        .actions(self => ({
-        setJexlFilters(f) {
-            self.jexlFilters = (0, mobx_state_tree_1.cast)(f);
-        },
-        setRowHeight(arg) {
-            self.rowHeightSetting = arg;
-        },
-        setHoveredGenotype(arg) {
-            self.hoveredGenotype = arg;
-        },
-        setFeatures(f) {
-            self.featuresVolatile = f;
-        },
-        setLayout(layout) {
-            self.layout = layout;
-        },
-        clearLayout() {
-            self.layout = [];
-        },
-        setSourcesLoading(str) {
-            if (self.sourcesLoadingStopToken) {
-                (0, stopToken_1.stopStopToken)(self.sourcesLoadingStopToken);
-            }
-            self.sourcesLoadingStopToken = str;
-        },
-        setSimplifiedFeaturesLoading(str) {
-            if (self.simplifiedFeaturesStopToken) {
-                (0, stopToken_1.stopStopToken)(self.simplifiedFeaturesStopToken);
-            }
-            self.simplifiedFeaturesStopToken = str;
-        },
-        setSources(sources) {
-            if (!(0, fast_deep_equal_1.default)(sources, self.sourcesVolatile)) {
-                self.sourcesVolatile = sources;
-            }
-        },
-        setMafFilter(arg) {
-            self.minorAlleleFrequencyFilter = arg;
-        },
-        setShowSidebarLabels(arg) {
-            self.showSidebarLabelsSetting = arg;
-        },
-        setPhasedMode(arg) {
-            self.renderingMode = arg;
-        },
-        setAutoHeight(arg) {
-            self.autoHeight = arg;
-        },
-        setHasPhased(arg) {
-            self.hasPhased = arg;
-        },
-        setSampleInfo(arg) {
-            if (!(0, fast_deep_equal_1.default)(arg, self.sampleInfo)) {
-                self.sampleInfo = arg;
-            }
-        },
-        setReferenceDrawingMode(arg) {
-            self.referenceDrawingMode = arg;
-        },
-    }))
-        .views(self => ({
-        get activeFilters() {
-            var _a;
-            return ((_a = self.jexlFilters) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jexlFilters').map((r) => `jexl:${r}`));
-        },
-        get preSources() {
-            return self.layout.length ? self.layout : self.sourcesVolatile;
-        },
-        get sourcesWithoutLayout() {
-            return self.sourcesVolatile
-                ? (0, getSources_1.getSources)({
-                    sources: self.sourcesVolatile,
-                    renderingMode: self.renderingMode,
-                    sampleInfo: self.sampleInfo,
-                })
-                : undefined;
-        },
-        get sources() {
-            const sourcesWithLayout = self.layout.length
-                ? self.layout
-                : self.sourcesVolatile;
-            return sourcesWithLayout
-                ? (0, getSources_1.getSources)({
-                    sources: sourcesWithLayout,
-                    renderingMode: self.renderingMode,
-                    sampleInfo: self.sampleInfo,
-                })
-                : undefined;
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            get sourceMap() {
-                return self.sources
-                    ? Object.fromEntries(self.sources.map(source => [source.name, source]))
-                    : undefined;
-            },
-            get rowHeight() {
-                const { sources, autoHeight, rowHeightSetting, height } = self;
-                return autoHeight ? height / ((sources === null || sources === void 0 ? void 0 : sources.length) || 1) : rowHeightSetting;
-            },
-            adapterProps() {
-                const superProps = superRenderProps();
-                return {
-                    ...superProps,
-                    rpcDriverName: self.rpcDriverName,
-                    displayModel: self,
-                    config: self.rendererConfig,
-                };
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Show sidebar labels',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showSidebarLabelsSetting,
-                        onClick: () => {
-                            self.setShowSidebarLabels(!self.showSidebarLabelsSetting);
-                        },
-                    },
-                    {
-                        label: 'Row height',
-                        icon: Height_1.default,
-                        subMenu: [
-                            {
-                                label: 'Manually set row height',
-                                disabled: self.autoHeight,
-                                onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                        SetRowHeightDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                            {
-                                label: 'Auto-adjust to display height',
-                                type: 'checkbox',
-                                checked: self.autoHeight,
-                                onClick: () => {
-                                    self.setAutoHeight(!self.autoHeight);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Rendering mode',
-                        icon: Splitscreen_1.default,
-                        subMenu: [
-                            {
-                                label: 'Allele count',
-                                type: 'radio',
-                                checked: self.renderingMode === 'alleleCount',
-                                onClick: () => {
-                                    self.setPhasedMode('alleleCount');
-                                },
-                            },
-                            {
-                                label: `Phased${!self.hasPhased
-                                    ? ' (disabled, no phased variants found)'
-                                    : ''}`,
-                                disabled: !self.hasPhased,
-                                checked: self.renderingMode === 'phased',
-                                type: 'radio',
-                                onClick: () => {
-                                    self.setPhasedMode('phased');
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Reference mode',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                label: 'Fill background grey, skip reference allele mouseovers (helps with large overlapping SVs)',
-                                type: 'radio',
-                                checked: self.referenceDrawingMode === 'skip',
-                                onClick: () => {
-                                    self.setReferenceDrawingMode('skip');
-                                },
-                            },
-                            {
-                                label: "Don't fill background grey, only draw actual reference alleles as grey",
-                                type: 'radio',
-                                checked: self.referenceDrawingMode === 'draw',
-                                onClick: () => {
-                                    self.setReferenceDrawingMode('draw');
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Filter by',
-                        icon: FilterList_1.default,
-                        subMenu: [
-                            {
-                                label: 'Minor allele frequency',
-                                onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                        MAFFilterDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                            {
-                                label: 'Edit filters',
-                                onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                        AddFiltersDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Cluster by genotype',
-                        icon: Category_1.default,
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                ClusterDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Edit group colors/arrangement...',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                SetColorDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                ];
-            },
-        };
-    })
-        .views(self => ({
-        get canDisplayLabels() {
-            return self.rowHeight >= 8 && self.showSidebarLabelsSetting;
-        },
-        get totalHeight() {
-            var _a;
-            return self.rowHeight * (((_a = self.sources) === null || _a === void 0 ? void 0 : _a.length) || 1);
-        },
-        get featuresReady() {
-            return !!self.featuresVolatile;
-        },
-    }))
-        .views(self => ({
-        renderProps() {
-            const superProps = self.adapterProps();
-            return {
-                ...superProps,
-                notReady: superProps.notReady || !self.sources || !self.featuresReady,
-                height: self.height,
-                totalHeight: self.totalHeight,
-                renderingMode: self.renderingMode,
-                minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
-                lengthCutoffFilter: self.lengthCutoffFilter,
-                rowHeight: self.rowHeight,
-                sources: self.sources,
-                scrollTop: self.scrollTop,
-                referenceDrawingMode: self.referenceDrawingMode,
-                filters: new serializableFilterChain_1.default({
-                    filters: self.activeFilters,
-                }),
-            };
-        },
-    }));
-}

package/dist/shared/SharedVariantConfigSchema.d.ts

@@ -1,66 +0,0 @@
-export default function sharedVariantConfigFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minimalTicks: {
-        type: string;
-        defaultValue: boolean;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    numStdDev: {
-        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;
-    };
-}, 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/shared/SharedVariantConfigSchema.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = sharedVariantConfigFactory;
-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");
-function sharedVariantConfigFactory() {
-    return (0, configuration_1.ConfigurationSchema)('SharedVariantDisplay', {
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: mobx_state_tree_1.types.enumeration('Autoscale type', [
-                'global',
-                'local',
-                'globalsd',
-                'localsd',
-                'zscore',
-            ]),
-            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
-        },
-        minimalTicks: {
-            type: 'boolean',
-            defaultValue: false,
-            description: 'use the minimal amount of ticks',
-        },
-        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,
-        },
-        numStdDev: {
-            type: 'number',
-            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
-            defaultValue: 3,
-        },
-        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,
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}