@jbrowse/plugin-linear-genome-view/esm/LinearBasicDisplay/model.js

JBrowse 2 linear genome view

import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
import { types } from '@jbrowse/mobx-state-tree';
import { modelFactory as LinearFeatureDisplayModelFactory } from "../LinearFeatureDisplay/index.js";
function findSubMenu(items, label) {
    return items.find((item) => 'label' in item && item.label === label);
}
function stateModelFactory(configSchema) {
    return types
        .compose('LinearBasicDisplay', LinearFeatureDisplayModelFactory(configSchema), types.model({
        type: types.literal('LinearBasicDisplay'),
        trackGeneGlyphMode: types.maybe(types.string),
        trackSubfeatureLabels: types.maybe(types.string),
        trackDisplayDirectionalChevrons: types.maybe(types.boolean),
        configuration: ConfigurationReference(configSchema),
    }))
        .views(self => ({
        get geneGlyphMode() {
            return (self.trackGeneGlyphMode ??
                getConf(self, ['renderer', 'geneGlyphMode']));
        },
        get subfeatureLabels() {
            return (self.trackSubfeatureLabels ??
                getConf(self, ['renderer', 'subfeatureLabels']));
        },
        get displayDirectionalChevrons() {
            return (self.trackDisplayDirectionalChevrons ??
                getConf(self, ['renderer', 'displayDirectionalChevrons']));
        },
    }))
        .views(self => ({
        get rendererConfig() {
            const configBlob = getConf(self, ['renderer']) || {};
            const config = configBlob;
            return {
                ...config,
                showLabels: self.trackShowLabels ?? config.showLabels,
                showDescriptions: self.trackShowDescriptions ?? config.showDescriptions,
                subfeatureLabels: self.trackSubfeatureLabels ?? config.subfeatureLabels,
                displayMode: self.trackDisplayMode ?? config.displayMode,
                maxHeight: self.trackMaxHeight ?? config.maxHeight,
                geneGlyphMode: self.trackGeneGlyphMode ?? config.geneGlyphMode,
                displayDirectionalChevrons: self.trackDisplayDirectionalChevrons ??
                    config.displayDirectionalChevrons,
            };
        },
    }))
        .actions(self => ({
        setGeneGlyphMode(val) {
            self.trackGeneGlyphMode = val;
        },
        setSubfeatureLabels(val) {
            self.trackSubfeatureLabels = val;
        },
        toggleDisplayDirectionalChevrons() {
            self.trackDisplayDirectionalChevrons = !self.displayDirectionalChevrons;
        },
    }))
        .views(self => {
        const { filterMenuItems: superFilterMenuItems } = self;
        return {
            filterMenuItems() {
                const filters = self.activeFilters();
                return [
                    {
                        label: 'Show only genes',
                        type: 'checkbox',
                        checked: filters.includes("jexl:get(feature,'type')=='gene'"),
                        onClick: () => {
                            const geneFilter = "jexl:get(feature,'type')=='gene'";
                            if (filters.includes(geneFilter)) {
                                self.setJexlFilters(filters.filter(f => f !== geneFilter));
                            }
                            else {
                                self.setJexlFilters([...filters, geneFilter]);
                            }
                        },
                    },
                    ...superFilterMenuItems(),
                ];
            },
        };
    })
        .views(self => {
        const { trackMenuItems: superTrackMenuItems } = self;
        return {
            trackMenuItems() {
                const items = superTrackMenuItems();
                const showMenu = findSubMenu(items, 'Show...');
                if (showMenu) {
                    showMenu.subMenu = [
                        ...showMenu.subMenu,
                        {
                            label: 'Show chevrons',
                            type: 'checkbox',
                            checked: self.displayDirectionalChevrons,
                            onClick: () => {
                                self.toggleDisplayDirectionalChevrons();
                            },
                        },
                        {
                            label: 'Subfeature labels',
                            subMenu: ['none', 'below', 'overlay'].map(val => ({
                                label: val,
                                type: 'radio',
                                checked: self.subfeatureLabels === val,
                                onClick: () => {
                                    self.setSubfeatureLabels(val);
                                },
                            })),
                        },
                        {
                            label: 'Gene glyph',
                            subMenu: [
                                {
                                    value: 'all',
                                    label: 'All transcripts',
                                },
                                {
                                    value: 'longest',
                                    label: 'Longest transcript',
                                },
                                {
                                    value: 'longestCoding',
                                    label: 'Longest coding transcript',
                                },
                            ].map(({ value, label }) => ({
                                label,
                                type: 'radio',
                                checked: self.geneGlyphMode === value,
                                onClick: () => {
                                    self.setGeneGlyphMode(value);
                                },
                            })),
                        },
                    ];
                }
                return items;
            },
        };
    })
        .postProcessSnapshot(snap => {
        if (!snap) {
            return snap;
        }
        const { trackGeneGlyphMode, trackSubfeatureLabels, trackDisplayDirectionalChevrons, ...rest } = snap;
        return {
            ...rest,
            ...(trackGeneGlyphMode !== undefined ? { trackGeneGlyphMode } : {}),
            ...(trackSubfeatureLabels !== undefined
                ? { trackSubfeatureLabels }
                : {}),
            ...(trackDisplayDirectionalChevrons !== undefined
                ? { trackDisplayDirectionalChevrons }
                : {}),
        };
    });
}
export default stateModelFactory;