@jbrowse/plugin-linear-genome-view 4.3.0 → 5.0.0-beta.2

package/esm/LinearBasicDisplay/model.js

@@ -1,158 +0,0 @@
-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;

package/esm/LinearFeatureDisplay/components/AddFiltersDialog.d.ts

@@ -1,9 +0,0 @@
-declare const AddFiltersDialog: ({ model, handleClose, }: {
-    model: {
-        jexlFilters?: string[];
-        activeFilters: () => string[];
-        setJexlFilters: (arg?: string[]) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AddFiltersDialog;

package/esm/LinearFeatureDisplay/components/AddFiltersDialog.js

@@ -1,58 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useEffect, useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings';
-import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
-import { observer } from 'mobx-react';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    error: {
-        color: 'red',
-        fontSize: '0.8em',
-    },
-});
-function checkJexl(code) {
-    stringToJexlExpression(code);
-}
-const AddFiltersDialog = observer(function AddFiltersDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const { activeFilters } = model;
-    const [data, setData] = useState(activeFilters().join('\n'));
-    const [error, setError] = useState();
-    useEffect(() => {
-        try {
-            for (const line of data
-                .split('\n')
-                .map(line => line.trim())
-                .filter(line => !!line)) {
-                checkJexl(line);
-            }
-            setError(undefined);
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }, [data]);
-    return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters", children: [_jsxs(DialogContent, { children: [_jsxs("div", { children: ["Add filters, in jexl format, one per line, starting with the string jexl:. Examples:", ' ', _jsxs("ul", { children: [_jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'name')=='BRCA1'" }), " - show only feature where the name attribute is BRCA1"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:startsWith(get(feature,'name'),'PREFIX')" }), " - show only feature where the string 'PREFIX' is the prefix of feature name. endsWith also works"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:includes(get(feature,'name'),'PREFIX')" }), " - show only feature where the string 'PREFIX' is the prefix of feature name"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'type')=='gene'" }), " - show only gene type features in a GFF that has many other feature types"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'score') > 400" }), " - show only features that have a score greater than 400"] }), _jsxs("li", { children: [_jsx("code", { children: "jexl:get(feature,'end') - get(feature,'start') < 1000000" }), ' ', "- show only features with length less than 1Mbp"] })] }), _jsxs("p", { children: ["Please see", ' ', _jsx("a", { href: "https://jbrowse.org/jb2/docs/config_guides/jexl/", children: "Jexl" }), ' ', "documentation for more information"] })] }), error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsx(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
-                            setData(event.target.value);
-                        }, slotProps: {
-                            input: {
-                                classes: {
-                                    input: classes.textAreaFont,
-                                },
-                            },
-                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !!error, onClick: () => {
-                            model.setJexlFilters(data.split('\n'));
-                            handleClose();
-                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-export default AddFiltersDialog;

package/esm/LinearFeatureDisplay/components/SetMaxHeightDialog.d.ts

@@ -1,8 +0,0 @@
-declare const SetMaxHeightDialog: ({ model, handleClose, }: {
-    model: {
-        maxHeight?: number;
-        setMaxHeight: (arg?: number) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SetMaxHeightDialog;

package/esm/LinearFeatureDisplay/components/SetMaxHeightDialog.js

@@ -1,26 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-const useStyles = makeStyles()({
-    root: {
-        width: 500,
-    },
-});
-const SetMaxHeightDialog = observer(function SetMaxHeightDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const { maxHeight = '' } = model;
-    const [max, setMax] = useState(`${maxHeight}`);
-    const ok = max !== '' && !Number.isNaN(+max);
-    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Set max track height", children: [_jsxs(DialogContent, { className: classes.root, children: [_jsx(Typography, { children: "Set max layout height for the track. For example, you can increase this if the layout says \"Max height reached\"" }), _jsx(TextField, { value: max, onChange: event => {
-                            setMax(event.target.value);
-                        }, placeholder: "Enter max score" }), !ok ? _jsx("div", { style: { color: 'red' }, children: "Invalid number" }) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {
-                            model.setMaxHeight(+max);
-                            handleClose();
-                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-export default SetMaxHeightDialog;

package/esm/LinearFeatureDisplay/configSchema.d.ts

@@ -1,32 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("@jbrowse/mobx-state-tree").IAnyModelType;
-}, 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>>;
-export default configSchemaFactory;

package/esm/LinearFeatureDisplay/configSchema.js

@@ -1,11 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { baseLinearDisplayConfigSchema } from "../BaseLinearDisplay/index.js";
-function configSchemaFactory(pluginManager) {
-    return ConfigurationSchema('LinearFeatureDisplay', {
-        renderer: pluginManager.pluggableConfigSchemaType('renderer'),
-    }, {
-        baseConfiguration: baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}
-export default configSchemaFactory;

package/esm/LinearFeatureDisplay/index.d.ts

@@ -1,3 +0,0 @@
-export { default as modelFactory } from './model.ts';
-export { default as configSchema } from './configSchema.ts';
-export type { LinearFeatureDisplayModel, LinearFeatureDisplayStateModel, } from './model.ts';

package/esm/LinearFeatureDisplay/index.js

@@ -1,2 +0,0 @@
-export { default as modelFactory } from "./model.js";
-export { default as configSchema } from "./configSchema.js";