@jbrowse/plugin-hic 3.7.0 → 4.0.1

package/dist/LinearHicDisplay/model.js

@@ -1,205 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = stateModelFactory;
-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_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearHicDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearHicDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        resolution: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
-        useLogScale: false,
-        colorScheme: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        activeNormalization: 'KR',
-        mode: 'triangular',
-    }))
-        .volatile(() => ({
-        availableNormalizations: undefined,
-    }))
-        .views(self => {
-        const { renderProps: superRenderProps } = self;
-        return {
-            get blockType() {
-                return 'dynamicBlocks';
-            },
-            get rendererTypeName() {
-                return 'HicRenderer';
-            },
-            renderProps() {
-                const config = self.rendererType.configSchema.create({
-                    ...(0, configuration_1.getConf)(self, 'renderer'),
-                    ...(self.colorScheme
-                        ? { color: 'jexl:interpolate(count,scale)' }
-                        : {}),
-                }, (0, mobx_state_tree_1.getEnv)(self));
-                return {
-                    ...superRenderProps(),
-                    config,
-                    displayHeight: self.mode === 'adjust' ? self.height : undefined,
-                    normalization: self.activeNormalization,
-                    rpcDriverName: self.rpcDriverName,
-                    displayModel: self,
-                    resolution: self.resolution,
-                    useLogScale: self.useLogScale,
-                    colorScheme: self.colorScheme,
-                };
-            },
-        };
-    })
-        .actions(self => ({
-        setResolution(n) {
-            self.resolution = n;
-        },
-        setUseLogScale(f) {
-            self.useLogScale = f;
-        },
-        setColorScheme(f) {
-            self.colorScheme = f;
-        },
-        setActiveNormalization(f) {
-            self.activeNormalization = f;
-        },
-        setAvailableNormalizations(f) {
-            self.availableNormalizations = f;
-        },
-        setMode(arg) {
-            self.mode = arg;
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems } = self;
-        return {
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Use log scale',
-                        type: 'checkbox',
-                        checked: self.useLogScale,
-                        onClick: () => {
-                            self.setUseLogScale(!self.useLogScale);
-                        },
-                    },
-                    {
-                        label: 'Rendering mode',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                label: 'Triangular',
-                                type: 'radio',
-                                checked: self.mode === 'triangular',
-                                onClick: () => {
-                                    self.setMode('triangular');
-                                },
-                            },
-                            {
-                                label: 'Adjust to height of display',
-                                type: 'radio',
-                                checked: self.mode === 'adjust',
-                                onClick: () => {
-                                    self.setMode('adjust');
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Color scheme',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                label: 'Fall',
-                                type: 'radio',
-                                checked: self.colorScheme === 'fall',
-                                onClick: () => {
-                                    self.setColorScheme('fall');
-                                },
-                            },
-                            {
-                                label: 'Viridis',
-                                type: 'radio',
-                                checked: self.colorScheme === 'viridis',
-                                onClick: () => {
-                                    self.setColorScheme('viridis');
-                                },
-                            },
-                            {
-                                label: 'Juicebox',
-                                type: 'radio',
-                                checked: self.colorScheme === 'juicebox',
-                                onClick: () => {
-                                    self.setColorScheme('juicebox');
-                                },
-                            },
-                            {
-                                label: 'Default',
-                                type: 'radio',
-                                checked: self.colorScheme === undefined,
-                                onClick: () => {
-                                    self.setColorScheme(undefined);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Resolution',
-                        subMenu: [
-                            {
-                                label: 'Finer resolution',
-                                onClick: () => {
-                                    self.setResolution(self.resolution * 2);
-                                },
-                            },
-                            {
-                                label: 'Coarser resolution',
-                                onClick: () => {
-                                    self.setResolution(self.resolution / 2);
-                                },
-                            },
-                        ],
-                    },
-                    ...(self.availableNormalizations
-                        ? [
-                            {
-                                label: 'Normalization scheme',
-                                subMenu: self.availableNormalizations.map(norm => ({
-                                    label: norm,
-                                    type: 'radio',
-                                    checked: norm === self.activeNormalization,
-                                    onClick: () => {
-                                        self.setActiveNormalization(norm);
-                                    },
-                                })),
-                            },
-                        ]
-                        : []),
-                ];
-            },
-        };
-    })
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                try {
-                    const { rpcManager } = (0, util_1.getSession)(self);
-                    const track = (0, util_1.getContainingTrack)(self);
-                    const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
-                    const { norms } = (await rpcManager.call((0, configuration_1.getConf)(track, 'trackId'), 'CoreGetInfo', {
-                        adapterConfig,
-                    }));
-                    if (norms) {
-                        self.setAvailableNormalizations(norms);
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    (0, util_1.getSession)(self).notifyError(`${e}`, e);
-                }
-            }));
-        },
-    }));
-}

package/dist/index.d.ts

@@ -1,7 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class HicPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-    configure(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,33 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const colord_1 = require("@jbrowse/core/util/colord");
-const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
-const HicAdapter_1 = __importDefault(require("./HicAdapter"));
-const HicRenderer_1 = __importDefault(require("./HicRenderer"));
-const HicTrack_1 = __importDefault(require("./HicTrack"));
-const LinearHicDisplay_1 = __importDefault(require("./LinearHicDisplay"));
-class HicPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'HicPlugin';
-    }
-    install(pluginManager) {
-        (0, HicAdapter_1.default)(pluginManager);
-        (0, HicRenderer_1.default)(pluginManager);
-        (0, HicTrack_1.default)(pluginManager);
-        (0, LinearHicDisplay_1.default)(pluginManager);
-        (0, GuessAdapter_1.default)(pluginManager);
-    }
-    configure(pluginManager) {
-        const { jexl } = pluginManager;
-        jexl.addFunction('alpha', (color, n) => color.alpha(n));
-        jexl.addFunction('hsl', (color) => (0, colord_1.colord)(color.toHsl()));
-        jexl.addFunction('colorString', (color) => color.toHex());
-        jexl.addFunction('interpolate', (count, scale) => scale(count));
-    }
-}
-exports.default = HicPlugin;