@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/LinearAlignmentsDisplay/model.d.ts

@@ -1,126 +0,0 @@
-import type { FilterBy } from '../shared/types';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { MenuItem } from '@jbrowse/core/ui';
-import type { Instance } from 'mobx-state-tree';
-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>>;
-} & {
-    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
-    SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
-    snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
-    type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
-}, {
-    rendererTypeName: string;
-    error: unknown;
-    message: string | undefined;
-} & {
-    readonly RenderingComponent: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: () => void;
-        blockState?: Record<string, any>;
-    }>;
-    readonly DisplayBlurb: React.FC<{
-        model: {
-            id: string;
-            type: string;
-            rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<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>>;
-        }, {
-            rendererTypeName: string;
-            error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
-    readonly adapterConfig: any;
-    readonly parentTrack: any;
-    renderProps(): any;
-    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | React.FC<any>;
-    trackMenuItems(): MenuItem[];
-    readonly viewMenuActions: MenuItem[];
-    regionCannotBeRendered(): null;
-} & {
-    setMessage(arg?: string): void;
-    setError(error?: unknown): void;
-    setRpcDriverName(rpcDriverName: string): void;
-    reload(): void;
-} & {
-    scrollTop: number;
-} & {
-    setScrollTop(scrollTop: number): void;
-    setSNPCoverageHeight(n: number): void;
-} & {
-    readonly height: any;
-    readonly featureIdUnderMouse: any;
-} & {
-    readonly pileupConf: any;
-    getFeatureByID(blockKey: string, id: string): any;
-    searchFeatureByID(id: string): any;
-    readonly features: any;
-    readonly DisplayBlurb: any;
-    readonly sortedBy: any;
-    readonly coverageConf: any;
-    notReady(): any;
-} & {
-    setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
-    setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
-    setPileupDisplay(configuration: AnyConfigurationModel): void;
-    setHeight(n: number): number;
-    setFilterBy(filter: FilterBy): void;
-    setLowerPanelType(type: string): void;
-    resizeHeight(distance: number): number;
-} & {
-    afterAttach(): void;
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<import("react/jsx-runtime").JSX.Element>;
-} & {
-    trackMenuItems(): MenuItem[];
-}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    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>>;
-} & {
-    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
-    SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
-    snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
-    type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: AnyConfigurationSchemaType;
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
-}>>, import("mobx-state-tree")._NotCustomized>;
-export default stateModelFactory;
-export type LinearAlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export type LinearAlignmentsDisplayModel = Instance<LinearAlignmentsDisplayStateModel>;

package/dist/LinearAlignmentsDisplay/model.js

@@ -1,222 +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 configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const alignmentsModel_1 = require("./alignmentsModel");
-const util_1 = require("./util");
-const minDisplayHeight = 20;
-function preCheck(self) {
-    const { PileupDisplay, SNPCoverageDisplay } = self;
-    return (PileupDisplay ||
-        (0, mobx_state_tree_1.isAlive)(PileupDisplay) ||
-        SNPCoverageDisplay ||
-        (0, mobx_state_tree_1.isAlive)(SNPCoverageDisplay));
-}
-function propagateColorBy(self) {
-    const { PileupDisplay, SNPCoverageDisplay } = self;
-    if (!preCheck(self) || !PileupDisplay.colorBy) {
-        return;
-    }
-    if (!(0, fast_deep_equal_1.default)(PileupDisplay.colorBy, SNPCoverageDisplay.colorBy)) {
-        SNPCoverageDisplay.setColorScheme({
-            ...PileupDisplay.colorBy,
-        });
-    }
-}
-function propagateFilterBy(self) {
-    const { PileupDisplay, SNPCoverageDisplay } = self;
-    if (!preCheck(self) || !PileupDisplay.filterBy) {
-        return;
-    }
-    if (!(0, fast_deep_equal_1.default)(PileupDisplay.filterBy, SNPCoverageDisplay.filterBy)) {
-        SNPCoverageDisplay.setFilterBy({
-            ...PileupDisplay.filterBy,
-        });
-    }
-}
-function stateModelFactory(pluginManager, configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, (0, alignmentsModel_1.LinearAlignmentsDisplayMixin)(pluginManager, configSchema))
-        .volatile(() => ({
-        scrollTop: 0,
-    }))
-        .actions(self => ({
-        setScrollTop(scrollTop) {
-            self.scrollTop = scrollTop;
-        },
-        setSNPCoverageHeight(n) {
-            self.snpCovHeight = n;
-        },
-    }))
-        .views(self => ({
-        get height() {
-            var _a;
-            return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
-        },
-        get featureIdUnderMouse() {
-            return (self.PileupDisplay.featureIdUnderMouse ||
-                self.SNPCoverageDisplay.featureIdUnderMouse);
-        },
-    }))
-        .views(self => ({
-        get pileupConf() {
-            const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
-            return {
-                ...conf,
-                type: self.lowerPanelType,
-                displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`,
-            };
-        },
-        getFeatureByID(blockKey, id) {
-            return self.PileupDisplay.getFeatureByID(blockKey, id);
-        },
-        searchFeatureByID(id) {
-            var _a, _b;
-            return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
-        },
-        get features() {
-            return self.PileupDisplay.features;
-        },
-        get DisplayBlurb() {
-            var _a;
-            return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
-        },
-        get sortedBy() {
-            return self.PileupDisplay.sortedBy;
-        },
-        get coverageConf() {
-            const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
-            return {
-                ...conf,
-                displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
-            };
-        },
-        notReady() {
-            var _a, _b;
-            return (((_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.renderProps().notReady) ||
-                ((_b = self.SNPCoverageDisplay) === null || _b === void 0 ? void 0 : _b.renderProps().notReady));
-        },
-    }))
-        .actions(self => ({
-        setSNPCoverageDisplay(configuration) {
-            self.SNPCoverageDisplay = {
-                type: 'LinearSNPCoverageDisplay',
-                configuration,
-                height: self.snpCovHeight,
-            };
-        },
-        setFeatureDensityStatsLimit(stats) {
-            self.PileupDisplay.setFeatureDensityStatsLimit(stats);
-            self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
-        },
-        setPileupDisplay(configuration) {
-            self.PileupDisplay = {
-                type: configuration.type || 'LinearPileupDisplay',
-                configuration,
-            };
-        },
-        setHeight(n) {
-            self.heightPreConfig = Math.max(n, minDisplayHeight);
-            return self.heightPreConfig;
-        },
-        setFilterBy(filter) {
-            self.PileupDisplay.setFilterBy(filter);
-            self.SNPCoverageDisplay.setFilterBy(filter);
-        },
-        setLowerPanelType(type) {
-            self.lowerPanelType = type;
-        },
-        resizeHeight(distance) {
-            const oldHeight = self.height;
-            const newHeight = this.setHeight(self.height + distance);
-            return newHeight - oldHeight;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                const { SNPCoverageDisplay, PileupDisplay, coverageConf, pileupConf, } = self;
-                if (!SNPCoverageDisplay) {
-                    self.setSNPCoverageDisplay(coverageConf);
-                }
-                else if (!(0, fast_deep_equal_1.default)(coverageConf, (0, mobx_state_tree_1.getSnapshot)(SNPCoverageDisplay.configuration))) {
-                    SNPCoverageDisplay.setHeight(self.snpCovHeight);
-                    SNPCoverageDisplay.setConfig(self.coverageConf);
-                }
-                if (!PileupDisplay || self.lowerPanelType !== PileupDisplay.type) {
-                    self.setPileupDisplay(pileupConf);
-                }
-                else if (!(0, fast_deep_equal_1.default)(pileupConf, (0, mobx_state_tree_1.getSnapshot)(PileupDisplay.configuration))) {
-                    PileupDisplay.setConfig(self.pileupConf);
-                }
-                propagateColorBy(self);
-                propagateFilterBy(self);
-            }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                self.setSNPCoverageHeight(self.SNPCoverageDisplay.height);
-            }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                self.PileupDisplay.setHeight(self.height - self.SNPCoverageDisplay.height);
-            }));
-        },
-        async renderSvg(opts) {
-            const pileupHeight = self.height - self.SNPCoverageDisplay.height;
-            await (0, mobx_1.when)(() => !self.notReady());
-            return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("g", { children: await self.SNPCoverageDisplay.renderSvg(opts) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})`, children: await self.PileupDisplay.renderSvg({
-                            ...opts,
-                            overrideHeight: pileupHeight,
-                        }) })] }));
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems } = self;
-        return {
-            trackMenuItems() {
-                if (!self.PileupDisplay) {
-                    return [];
-                }
-                const extra = (0, util_1.getLowerPanelDisplays)(pluginManager).map(d => ({
-                    type: 'radio',
-                    label: d.displayName,
-                    checked: d.name === self.PileupDisplay.type,
-                    onClick: () => {
-                        self.setLowerPanelType(d.name);
-                    },
-                }));
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        type: 'subMenu',
-                        label: 'Pileup settings',
-                        subMenu: self.PileupDisplay.trackMenuItems(),
-                    },
-                    {
-                        type: 'subMenu',
-                        label: 'SNPCoverage settings',
-                        subMenu: self.SNPCoverageDisplay.trackMenuItems(),
-                    },
-                    {
-                        type: 'subMenu',
-                        label: 'Replace lower panel with...',
-                        subMenu: extra,
-                    },
-                ];
-            },
-        };
-    })
-        .preProcessSnapshot(snap => {
-        if (!snap) {
-            return snap;
-        }
-        const { height, ...rest } = snap;
-        return { heightPreConfig: height, ...rest };
-    });
-}
-exports.default = stateModelFactory;

package/dist/LinearAlignmentsDisplay/util.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export declare function getLowerPanelDisplays(pluginManager: PluginManager): import("@jbrowse/core/pluggableElementTypes").DisplayType[];

package/dist/LinearAlignmentsDisplay/util.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getLowerPanelDisplays = getLowerPanelDisplays;
-function getLowerPanelDisplays(pluginManager) {
-    return pluginManager
-        .getDisplayElements()
-        .filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
-        .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; });
-}