@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -1,524 +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.SharedLinearPileupDisplayMixin = SharedLinearPileupDisplayMixin;
-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 tracks_1 = require("@jbrowse/core/util/tracks");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
-const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_2 = require("../util");
-const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
-const getUniqueTags_1 = require("../shared/getUniqueTags");
-const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
-const ColorByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTagDialog'))));
-const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/SetFeatureHeightDialog'))));
-const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/SetMaxHeightDialog'))));
-const rendererTypes = new Map([
-    ['pileup', 'PileupRenderer'],
-    ['svg', 'SvgFeatureRenderer'],
-]);
-function SharedLinearPileupDisplayMixin(configSchema) {
-    return mobx_state_tree_1.types
-        .compose(plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        featureHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        noSpacing: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        fadeLikelihood: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        trackMaxHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        colorBySetting: mobx_state_tree_1.types.frozen(),
-        filterBySetting: mobx_state_tree_1.types.frozen(),
-        jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
-        hideSmallIndelsSetting: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-    }))
-        .volatile(() => ({
-        colorTagMap: mobx_1.observable.map({}),
-        featureUnderMouseVolatile: undefined,
-        tagsReady: false,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-    }))
-        .views(self => ({
-        get autorunReady() {
-            const view = (0, util_1.getContainingView)(self);
-            return view.initialized && self.statsReadyAndRegionNotTooLarge;
-        },
-        get hideSmallIndels() {
-            return self.hideSmallIndelsSetting;
-        },
-    }))
-        .actions(self => ({
-        setTagsReady(flag) {
-            self.tagsReady = flag;
-        },
-        setMaxHeight(n) {
-            self.trackMaxHeight = n;
-        },
-        setFeatureHeight(n) {
-            self.featureHeight = n;
-        },
-        setNoSpacing(flag) {
-            self.noSpacing = flag;
-        },
-        setColorScheme(colorScheme) {
-            self.colorTagMap = mobx_1.observable.map({});
-            self.colorBySetting = {
-                ...colorScheme,
-            };
-            if (colorScheme.tag) {
-                self.tagsReady = false;
-            }
-        },
-        updateColorTagMap(uniqueTag) {
-            const colorPalette = [
-                '#BBCCEE',
-                'pink',
-                '#CCDDAA',
-                '#EEEEBB',
-                '#FFCCCC',
-                'lightblue',
-                'lightgreen',
-                'tan',
-                '#CCEEFF',
-                'lightsalmon',
-            ];
-            for (const value of uniqueTag) {
-                if (!self.colorTagMap.has(value)) {
-                    const totalKeys = [...self.colorTagMap.keys()].length;
-                    self.colorTagMap.set(value, colorPalette[totalKeys]);
-                }
-            }
-        },
-        setFeatureUnderMouse(feat) {
-            self.featureUnderMouseVolatile = feat;
-        },
-        selectFeature(feature) {
-            const session = (0, util_1.getSession)(self);
-            if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', {
-                    featureData: feature.toJSON(),
-                    view: (0, util_1.getContainingView)(self),
-                    track: (0, util_1.getContainingTrack)(self),
-                });
-                session.showWidget(featureWidget);
-            }
-            session.setSelection(feature);
-        },
-        setConfig(conf) {
-            self.configuration = conf;
-        },
-        setFilterBy(filter) {
-            self.filterBySetting = {
-                ...filter,
-            };
-        },
-        setJexlFilters(filters) {
-            self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
-        },
-        setHideSmallIndels(arg) {
-            self.hideSmallIndelsSetting = arg;
-        },
-    }))
-        .views(self => ({
-        copyFeatureToClipboard(feature) {
-            const { uniqueId, ...rest } = feature.toJSON();
-            const session = (0, util_1.getSession)(self);
-            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
-            session.notify('Copied to clipboard', 'success');
-        },
-        get rendererConfig() {
-            const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
-            const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
-            return self.rendererType.configSchema.create({
-                ...configBlob,
-                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
-                ...(height !== undefined ? { height } : {}),
-                ...(noSpacing !== undefined ? { noSpacing } : {}),
-                ...(maxHeight !== undefined ? { maxHeight } : {}),
-            }, (0, util_1.getEnv)(self));
-        },
-    }))
-        .views(self => ({
-        get maxHeight() {
-            return (0, configuration_1.readConfObject)(self.rendererConfig, 'maxHeight');
-        },
-        get featureHeightSetting() {
-            return (0, configuration_1.readConfObject)(self.rendererConfig, 'height');
-        },
-        get featureUnderMouse() {
-            return self.featureUnderMouseVolatile;
-        },
-        renderReady() {
-            return self.tagsReady;
-        },
-        get filters() {
-            return new serializableFilterChain_1.default({ filters: self.jexlFilters });
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            get rendererTypeName() {
-                const viewName = (0, configuration_1.getConf)(self, 'defaultRendering');
-                const rendererType = rendererTypes.get(viewName);
-                if (!rendererType) {
-                    throw new Error(`unknown alignments view name ${viewName}`);
-                }
-                return rendererType;
-            },
-            contextMenuItems() {
-                const feat = self.contextMenuFeature;
-                return feat
-                    ? [
-                        {
-                            label: 'Open feature details',
-                            icon: MenuOpen_1.default,
-                            onClick: () => {
-                                self.clearFeatureSelection();
-                                self.selectFeature(feat);
-                            },
-                        },
-                        {
-                            label: 'Copy info to clipboard',
-                            icon: ContentCopy_1.default,
-                            onClick: () => {
-                                self.copyFeatureToClipboard(feat);
-                            },
-                        },
-                    ]
-                    : [];
-            },
-            get DisplayBlurb() {
-                return LinearPileupDisplayBlurb_1.default;
-            },
-            renderPropsPre() {
-                const { colorTagMap, colorBy, filterBy, rpcDriverName } = self;
-                const superProps = superRenderProps();
-                return {
-                    ...superProps,
-                    notReady: superProps.notReady || !self.renderReady(),
-                    rpcDriverName,
-                    displayModel: self,
-                    colorBy,
-                    filterBy,
-                    filters: self.filters,
-                    colorTagMap: Object.fromEntries(colorTagMap.toJSON()),
-                    config: self.rendererConfig,
-                    async onFeatureClick(_, featureId) {
-                        const session = (0, util_1.getSession)(self);
-                        const { rpcManager } = session;
-                        try {
-                            const f = featureId || self.featureIdUnderMouse;
-                            if (!f) {
-                                self.clearFeatureSelection();
-                            }
-                            else {
-                                const sessionId = (0, tracks_1.getRpcSessionId)(self);
-                                const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
-                                    featureId: f,
-                                    sessionId,
-                                    layoutId: (0, util_1.getContainingTrack)(self).id,
-                                    rendererType: 'PileupRenderer',
-                                }));
-                                if ((0, mobx_state_tree_1.isAlive)(self) && feature) {
-                                    self.selectFeature(new util_1.SimpleFeature(feature));
-                                }
-                            }
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notifyError(`${e}`, e);
-                        }
-                    },
-                    onClick() {
-                        self.clearFeatureSelection();
-                    },
-                    async onFeatureContextMenu(_, featureId) {
-                        const session = (0, util_1.getSession)(self);
-                        const { rpcManager } = session;
-                        try {
-                            const f = featureId || self.featureIdUnderMouse;
-                            if (!f) {
-                                self.clearFeatureSelection();
-                            }
-                            else {
-                                const sessionId = (0, tracks_1.getRpcSessionId)(self);
-                                const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
-                                    featureId: f,
-                                    sessionId,
-                                    layoutId: (0, util_1.getContainingTrack)(self).id,
-                                    rendererType: 'PileupRenderer',
-                                }));
-                                if (feature) {
-                                    self.setContextMenuFeature(new util_1.SimpleFeature(feature));
-                                }
-                            }
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notifyError(`${e}`, e);
-                        }
-                    },
-                };
-            },
-            colorSchemeSubMenuItems() {
-                return [
-                    {
-                        label: 'Normal',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'normal',
-                            });
-                        },
-                    },
-                    {
-                        label: 'Mapping quality',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'mappingQuality',
-                            });
-                        },
-                    },
-                    {
-                        label: 'Strand',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'strand',
-                            });
-                        },
-                    },
-                    {
-                        label: 'Per-base quality',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'perBaseQuality',
-                            });
-                        },
-                    },
-                    {
-                        label: 'Per-base lettering',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'perBaseLettering',
-                            });
-                        },
-                    },
-                    {
-                        label: 'First-of-pair strand',
-                        onClick: () => {
-                            self.setColorScheme({
-                                type: 'stranded',
-                            });
-                        },
-                    },
-                    {
-                        label: 'Color by tag...',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                ColorByTagDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                ];
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Set feature height...',
-                        priority: 1,
-                        subMenu: [
-                            {
-                                label: 'Normal',
-                                onClick: () => {
-                                    self.setFeatureHeight(7);
-                                    self.setNoSpacing(false);
-                                },
-                            },
-                            {
-                                label: 'Compact',
-                                onClick: () => {
-                                    self.setFeatureHeight(2);
-                                    self.setNoSpacing(true);
-                                },
-                            },
-                            {
-                                label: 'Manually set height',
-                                onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                        SetFeatureHeightDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Hide small indels (<10bp)',
-                        priority: -1,
-                        type: 'checkbox',
-                        checked: self.hideSmallIndels,
-                        onClick: () => {
-                            self.setHideSmallIndels(!self.hideSmallIndels);
-                        },
-                    },
-                    {
-                        label: 'Set max height...',
-                        priority: -1,
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                SetMaxHeightDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                    {
-                        label: 'Filter by...',
-                        icon: ClearAll_1.default,
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                FilterByTagDialog,
-                                {
-                                    model: self,
-                                    handleClose,
-                                },
-                            ]);
-                        },
-                    },
-                ];
-            },
-        };
-    })
-        .views(self => ({
-        renderProps() {
-            return self.renderPropsPre();
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, util_2.createAutorun)(self, async () => {
-                const view = (0, util_1.getContainingView)(self);
-                if (!self.autorunReady) {
-                    return;
-                }
-                const { colorBy, tagsReady } = self;
-                const { staticBlocks } = view;
-                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) && !tagsReady) {
-                    const vals = await (0, getUniqueTags_1.getUniqueTags)({
-                        self,
-                        tag: colorBy.tag,
-                        blocks: staticBlocks,
-                    });
-                    if ((0, mobx_state_tree_1.isAlive)(self)) {
-                        self.updateColorTagMap(vals);
-                        self.setTagsReady(true);
-                    }
-                }
-                else {
-                    self.setTagsReady(true);
-                }
-            }, { delay: 1000 });
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                var _a;
-                const session = (0, util_1.getSession)(self);
-                try {
-                    const featureId = self.featureIdUnderMouse;
-                    if (((_a = self.featureUnderMouse) === null || _a === void 0 ? void 0 : _a.id()) !== featureId) {
-                        if (!featureId) {
-                            self.setFeatureUnderMouse(undefined);
-                        }
-                        else {
-                            const sessionId = (0, tracks_1.getRpcSessionId)(self);
-                            const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
-                                featureId,
-                                sessionId,
-                                layoutId: (0, util_1.getContainingTrack)(self).id,
-                                rendererType: 'PileupRenderer',
-                            }));
-                            if ((0, mobx_state_tree_1.isAlive)(self) &&
-                                feature &&
-                                self.featureIdUnderMouse === feature.uniqueId) {
-                                self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
-                            }
-                        }
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    session.notifyError(`${e}`, e);
-                }
-            }));
-        },
-    }))
-        .preProcessSnapshot(snap => {
-        if (snap) {
-            const { colorBy, colorBySetting, filterBySetting, filterBy, ...rest } = snap;
-            return {
-                ...rest,
-                filterBySetting: filterBySetting || filterBy,
-                colorBySetting: colorBySetting || colorBy,
-            };
-        }
-        return snap;
-    });
-}

package/dist/LinearPileupDisplay/components/ColorByTagDialog.d.ts

@@ -1,11 +0,0 @@
-interface Tag {
-    type: string;
-    tag: string;
-}
-declare const ColorByTagDialog: ({ model, handleClose, }: {
-    model: {
-        setColorScheme: (arg: Tag) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ColorByTagDialog;

package/dist/LinearPileupDisplay/components/ColorByTagDialog.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const ColorByTagDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    const [tag, setTag] = (0, react_1.useState)('');
-    const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { style: { overflowX: 'hidden' }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Enter tag to color by: " }), (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: tag, onChange: event => {
-                        setTag(event.target.value);
-                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", slotProps: {
-                        htmlInput: { maxLength: 2 },
-                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                                model.setColorScheme({ type: 'tag', tag });
-                                handleClose();
-                            }, disabled: !validTag, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }) }));
-});
-exports.default = ColorByTagDialog;

package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts

@@ -1,10 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-declare const GroupByTagDialog: (props: {
-    model: {
-        adapterConfig: AnyConfigurationModel;
-        configuration: AnyConfigurationModel;
-    } & IAnyStateTreeNode;
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default GroupByTagDialog;