@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.1

package/dist/LinearComparativeView/model.js

@@ -1,238 +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 });
-const react_1 = require("react");
-const BaseViewModel_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/models/BaseViewModel"));
-const util_1 = require("@jbrowse/core/util");
-const mst_1 = require("@jbrowse/core/util/types/mst");
-const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
-function stateModelFactory(pluginManager) {
-    var _a;
-    const LinearSyntenyViewHelper = (_a = pluginManager.getViewType('LinearSyntenyViewHelper')) === null || _a === void 0 ? void 0 : _a.stateModel;
-    return mobx_state_tree_1.types
-        .compose('LinearComparativeView', BaseViewModel_1.default, mobx_state_tree_1.types.model({
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('LinearComparativeView'),
-        trackSelectorType: 'hierarchical',
-        showIntraviewLinks: true,
-        linkViews: false,
-        interactiveOverlay: false,
-        showDynamicControls: true,
-        levels: mobx_state_tree_1.types.array(LinearSyntenyViewHelper),
-        views: mobx_state_tree_1.types.array(pluginManager.getViewType('LinearGenomeView')
-            .stateModel),
-        viewTrackConfigs: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('track')),
-    }))
-        .volatile(() => ({
-        width: undefined,
-    }))
-        .views(self => ({
-        get initialized() {
-            return (self.width !== undefined &&
-                self.views.length > 0 &&
-                self.views.every(view => view.initialized));
-        },
-        get refNames() {
-            return self.views.map(v => [
-                ...new Set(v.staticBlocks.map(m => m.refName)),
-            ]);
-        },
-        get assemblyNames() {
-            return [...new Set(self.views.flatMap(v => v.assemblyNames))];
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            const actions = new Set([
-                'horizontalScroll',
-                'zoomTo',
-                'setScaleFactor',
-            ]);
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_state_tree_1.onAction)(self, param => {
-                if (self.linkViews) {
-                    const { name, path, args } = param;
-                    if (actions.has(name) && path) {
-                        this.onSubviewAction(name, path, args);
-                    }
-                }
-            }));
-        },
-        beforeDestroy() {
-            var _a;
-            const session = (0, util_1.getSession)(self);
-            for (const name of self.assemblyNames) {
-                (_a = session.removeTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, name);
-            }
-        },
-        onSubviewAction(actionName, path, args) {
-            for (const view of self.views) {
-                const ret = (0, mobx_state_tree_1.getPath)(view);
-                if (!ret.endsWith(path)) {
-                    view[actionName](args === null || args === void 0 ? void 0 : args[0]);
-                }
-            }
-        },
-        setWidth(newWidth) {
-            self.width = newWidth;
-        },
-        setViews(views) {
-            self.views = (0, mobx_state_tree_1.cast)(views);
-            const levels = [];
-            for (let i = 0; i < views.length - 1; i++) {
-                levels.push({ level: i });
-            }
-            self.levels = (0, mobx_state_tree_1.cast)(levels);
-        },
-        removeView(view) {
-            self.views.remove(view);
-        },
-        setLevelHeight(newHeight, level = 0) {
-            const l = self.levels[level];
-            l.setHeight(newHeight);
-            return l.height;
-        },
-        setLinkViews(arg) {
-            self.linkViews = arg;
-        },
-        setShowDynamicControls(arg) {
-            self.showDynamicControls = arg;
-        },
-        activateTrackSelector(level) {
-            if (self.trackSelectorType === 'hierarchical') {
-                const session = (0, util_1.getSession)(self);
-                if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                    const selector = session.addWidget('HierarchicalTrackSelectorWidget', 'hierarchicalTrackSelector', {
-                        view: self.levels[level],
-                    });
-                    session.showWidget(selector);
-                    return selector;
-                }
-            }
-            throw new Error(`invalid track selector type ${self.trackSelectorType}`);
-        },
-        toggleTrack(trackId, level = 0) {
-            var _a;
-            (_a = self.levels[level]) === null || _a === void 0 ? void 0 : _a.toggleTrack(trackId);
-        },
-        showTrack(trackId, level = 0, initialSnapshot = {}) {
-            if (!self.levels[level]) {
-                self.levels[level] = (0, mobx_state_tree_1.cast)({ level });
-            }
-            self.levels[level].showTrack(trackId, initialSnapshot);
-        },
-        hideTrack(trackId, level = 0) {
-            var _a;
-            (_a = self.levels[level]) === null || _a === void 0 ? void 0 : _a.hideTrack(trackId);
-        },
-        squareView() {
-            const average = (0, util_1.avg)(self.views.map(v => v.bpPerPx));
-            for (const view of self.views) {
-                const center = view.pxToBp(view.width / 2);
-                view.setNewView(average, view.offsetPx);
-                if (center.refName) {
-                    view.centerAt(center.coord, center.refName, center.index);
-                }
-            }
-        },
-        clearView() {
-            self.views = (0, mobx_state_tree_1.cast)([]);
-            self.levels = (0, mobx_state_tree_1.cast)([]);
-        },
-    }))
-        .views(() => ({
-        headerMenuItems() {
-            return [];
-        },
-    }))
-        .views(self => ({
-        menuItems() {
-            return [
-                {
-                    label: 'Return to import form',
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            ReturnToImportFormDialog,
-                            {
-                                model: self,
-                                handleClose,
-                            },
-                        ]);
-                    },
-                    icon: FolderOpen_1.default,
-                },
-            ];
-        },
-        rubberBandMenuItems() {
-            return [
-                {
-                    label: 'Zoom to region(s)',
-                    onClick: () => {
-                        for (const view of self.views) {
-                            const { leftOffset, rightOffset } = view;
-                            if (leftOffset && rightOffset) {
-                                view.moveTo(leftOffset, rightOffset);
-                            }
-                        }
-                    },
-                },
-            ];
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                if (self.width) {
-                    for (const view of self.views) {
-                        view.setWidth(self.width);
-                    }
-                }
-            }));
-        },
-    }))
-        .preProcessSnapshot(snap => {
-        const { tracks, levels = [{ tracks, level: 0 }], ...rest } = snap || {};
-        return {
-            ...rest,
-            levels,
-        };
-    });
-}
-exports.default = stateModelFactory;

package/dist/LinearReadVsRef/LinearReadVsRef.d.ts

@@ -1,6 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export default function ReadVsRefDialog({ track, feature: preFeature, handleClose, }: {
-    feature: Feature;
-    handleClose: () => void;
-    track: any;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -1,241 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ReadVsRefDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const { featurizeSA, getClip, getLength, getLengthSansClipping, getTag } = plugin_alignments_1.MismatchParser;
-const useStyles = (0, mui_1.makeStyles)()({
-    root: {
-        width: 300,
-    },
-});
-function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
-    const { classes } = useStyles();
-    const [windowSizeText, setWindowSize] = (0, react_1.useState)('0');
-    const [error, setError] = (0, react_1.useState)();
-    const [primaryFeature, setPrimaryFeature] = (0, react_1.useState)();
-    const windowSize = +windowSizeText;
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            setError(undefined);
-            try {
-                if (preFeature.get('flags') & 2048) {
-                    const SA = getTag(preFeature, 'SA') || '';
-                    const primaryAln = SA.split(';')[0];
-                    const [saRef, saStart] = primaryAln.split(',');
-                    const { rpcManager } = (0, util_1.getSession)(track);
-                    const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
-                    const sessionId = (0, tracks_1.getRpcSessionId)(track);
-                    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-                        adapterConfig,
-                        sessionId,
-                        regions: [
-                            {
-                                refName: saRef,
-                                start: +saStart - 1,
-                                end: +saStart,
-                            },
-                        ],
-                    }));
-                    const result = feats.find(f => f.get('name') === preFeature.get('name') &&
-                        !(f.get('flags') & 2048) &&
-                        !(f.get('flags') & 256));
-                    if (result) {
-                        setPrimaryFeature(result);
-                    }
-                    else {
-                        throw new Error('primary feature not found');
-                    }
-                }
-                else {
-                    setPrimaryFeature(preFeature);
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [preFeature, track]);
-    function onSubmit() {
-        var _a;
-        try {
-            if (!primaryFeature) {
-                return;
-            }
-            const feature = primaryFeature;
-            const session = (0, util_1.getSession)(track);
-            const view = (0, util_1.getContainingView)(track);
-            const cigar = feature.get('CIGAR');
-            const flags = feature.get('flags');
-            const origStrand = feature.get('strand');
-            const SA = getTag(feature, 'SA') || '';
-            const readName = feature.get('name');
-            const clipPos = getClip(cigar, 1);
-            const readAssembly = `${readName}_assembly_${Date.now()}`;
-            const [trackAssembly] = (0, configuration_1.getConf)(track, 'assemblyNames');
-            const assemblyNames = [trackAssembly, readAssembly];
-            const trackId = `track-${Date.now()}`;
-            const trackName = `${readName}_vs_${trackAssembly}`;
-            const { assemblyManager } = session;
-            const assembly = assemblyManager.get(trackAssembly);
-            if (!assembly) {
-                throw new Error('assembly not found');
-            }
-            const suppAlns = featurizeSA(SA, feature.id(), origStrand, readName, true);
-            const feat = feature.toJSON();
-            feat.clipPos = clipPos;
-            feat.strand = 1;
-            feat.mate = {
-                refName: readName,
-                start: clipPos,
-                end: clipPos + getLengthSansClipping(cigar),
-            };
-            const totalLength = flags & 2048 ? getLength(suppAlns[0].CIGAR) : getLength(cigar);
-            const features = [feat, ...suppAlns];
-            for (const [idx, f] of features.entries()) {
-                f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
-                f.syntenyId = idx;
-                f.mate.syntenyId = idx;
-                f.mate.uniqueId = `${f.uniqueId}_mate`;
-            }
-            features.sort((a, b) => a.clipPos - b.clipPos);
-            const featSeq = feature.get('seq');
-            const configFeatureStore = [...features, ...features.map(f => f.mate)];
-            const expand = 2 * windowSize;
-            const refLen = features.reduce((a, f) => a + f.end - f.start + expand, 0);
-            const seqTrackId = `${readName}_${Date.now()}`;
-            const sequenceTrackConf = (0, configuration_1.getConf)(assembly, 'sequence');
-            const lgvRegions = (0, util_1.gatherOverlaps)(features.map(f => ({
-                ...f,
-                start: Math.max(0, f.start - windowSize),
-                end: f.end + windowSize,
-                assemblyName: trackAssembly,
-            })));
-            (_a = session.addTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, {
-                name: readAssembly,
-                sequence: {
-                    type: 'ReferenceSequenceTrack',
-                    name: 'Read sequence',
-                    trackId: seqTrackId,
-                    assemblyNames: [readAssembly],
-                    adapter: {
-                        type: 'FromConfigSequenceAdapter',
-                        noAssemblyManager: true,
-                        features: [
-                            {
-                                start: 0,
-                                end: totalLength,
-                                seq: featSeq || '',
-                                refName: readName,
-                                uniqueId: `${Math.random()}`,
-                            },
-                        ],
-                    },
-                },
-            });
-            session.addView('LinearSyntenyView', {
-                type: 'LinearSyntenyView',
-                views: [
-                    {
-                        type: 'LinearGenomeView',
-                        hideHeader: true,
-                        offsetPx: 0,
-                        bpPerPx: refLen / view.width,
-                        displayedRegions: lgvRegions,
-                        tracks: [
-                            {
-                                id: `${Math.random()}`,
-                                type: 'ReferenceSequenceTrack',
-                                assemblyNames: [trackAssembly],
-                                configuration: sequenceTrackConf.trackId,
-                                displays: [
-                                    {
-                                        id: `${Math.random()}`,
-                                        type: 'LinearReferenceSequenceDisplay',
-                                        showReverse: true,
-                                        showTranslation: false,
-                                        height: 35,
-                                        configuration: `${seqTrackId}-LinearReferenceSequenceDisplay`,
-                                    },
-                                ],
-                            },
-                        ],
-                    },
-                    {
-                        type: 'LinearGenomeView',
-                        hideHeader: true,
-                        offsetPx: 0,
-                        bpPerPx: totalLength / view.width,
-                        displayedRegions: [
-                            {
-                                assemblyName: readAssembly,
-                                start: 0,
-                                end: totalLength,
-                                refName: readName,
-                            },
-                        ],
-                        tracks: [
-                            {
-                                id: `${Math.random()}`,
-                                type: 'ReferenceSequenceTrack',
-                                configuration: seqTrackId,
-                                displays: [
-                                    {
-                                        id: `${Math.random()}`,
-                                        type: 'LinearReferenceSequenceDisplay',
-                                        showReverse: true,
-                                        showTranslation: false,
-                                        height: 35,
-                                        configuration: `${seqTrackId}-LinearReferenceSequenceDisplay`,
-                                    },
-                                ],
-                            },
-                        ],
-                    },
-                ],
-                viewTrackConfigs: [
-                    {
-                        type: 'SyntenyTrack',
-                        assemblyNames,
-                        adapter: {
-                            type: 'FromConfigAdapter',
-                            features: configFeatureStore,
-                        },
-                        trackId,
-                        name: trackName,
-                    },
-                ],
-                tracks: [
-                    {
-                        configuration: trackId,
-                        type: 'SyntenyTrack',
-                        displays: [
-                            {
-                                type: 'LinearSyntenyDisplay',
-                                configuration: `${trackId}-LinearSyntenyDisplay`,
-                            },
-                        ],
-                    },
-                ],
-                displayName: `${readName} vs ${trackAssembly}`,
-            });
-            handleClose();
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set window size", children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: error ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` })) : !primaryFeature ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "To accurately perform comparison we are fetching the primary alignment. Loading primary feature..." }), (0, jsx_runtime_1.jsx)(material_1.CircularProgress, {})] })) : ((0, jsx_runtime_1.jsxs)("div", { className: classes.root, children: [primaryFeature.get('flags') & 256 ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { style: { color: 'orange' }, children: "Note: You selected a secondary alignment (which generally does not have SA tags or SEQ fields) so do a full reconstruction of the alignment" })) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Show an extra window size around each part of the split alignment. Using a larger value can allow you to see more genomic context." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: windowSize, onChange: event => {
-                                setWindowSize(event.target.value);
-                            }, label: "Set window size" })] })) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" }), (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit, children: "Submit" })] })] }));
-}

package/dist/LinearReadVsRef/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LinearReadVsRefMenuItemF(pm: PluginManager): void;

package/dist/LinearReadVsRef/index.js

@@ -1,86 +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.default = LinearReadVsRefMenuItemF;
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-const ReadVsRefDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinearReadVsRef'))));
-function isDisplay(elt) {
-    return elt.name === 'LinearPileupDisplay';
-}
-function LinearReadVsRefMenuItemF(pm) {
-    pm.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
-        if (!isDisplay(pluggableElement)) {
-            return pluggableElement;
-        }
-        pluggableElement.stateModel = pluggableElement.stateModel.extend(self => {
-            const superContextMenuItems = self.contextMenuItems;
-            return {
-                views: {
-                    contextMenuItems() {
-                        const feature = self.contextMenuFeature;
-                        const track = (0, util_1.getContainingTrack)(self);
-                        return [
-                            ...superContextMenuItems(),
-                            ...(feature
-                                ? [
-                                    {
-                                        label: 'Linear read vs ref',
-                                        icon: Add_1.default,
-                                        onClick: () => {
-                                            (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                                ReadVsRefDialog,
-                                                {
-                                                    track,
-                                                    feature,
-                                                    handleClose,
-                                                },
-                                            ]);
-                                        },
-                                    },
-                                ]
-                                : []),
-                        ];
-                    },
-                },
-            };
-        });
-        return pluggableElement;
-    });
-}

package/dist/LinearSyntenyDisplay/afterAttach.d.ts

@@ -1,2 +0,0 @@
-import type { LinearSyntenyDisplayModel } from './model';
-export declare function doAfterAttach(self: LinearSyntenyDisplayModel): void;

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -1,104 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.doAfterAttach = doAfterAttach;
-const util_1 = require("@jbrowse/core/util");
-const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
-const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const drawSynteny_1 = require("./drawSynteny");
-function doAfterAttach(self) {
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-        var _a, _b;
-        const view = (0, util_1.getContainingView)(self);
-        if (!view.initialized ||
-            !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
-            return;
-        }
-        const ctx1 = (_a = self.mainCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
-        const ctx3 = (_b = self.cigarClickMapCanvas) === null || _b === void 0 ? void 0 : _b.getContext('2d');
-        if (!ctx1 || !ctx3) {
-            return;
-        }
-        const { alpha } = self;
-        const height = self.height;
-        const width = view.width;
-        ctx1.clearRect(0, 0, width, height);
-        (0, drawSynteny_1.drawRef)(self, ctx1);
-        (0, drawSynteny_1.drawCigarClickMap)(self, ctx3);
-    }));
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-        const view = (0, util_1.getContainingView)(self);
-        if (!view.initialized ||
-            !view.views.every(a => a.displayedRegions.length > 0 && a.initialized)) {
-            return;
-        }
-        const { clickId, mouseoverId } = self;
-        (0, drawSynteny_1.drawMouseoverClickMap)(self);
-    }));
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => {
-        const view = (0, util_1.getContainingView)(self);
-        return {
-            bpPerPx: view.views.map(v => v.bpPerPx),
-            displayedRegions: JSON.stringify(view.views.map(v => v.displayedRegions)),
-            features: self.features,
-            initialized: view.initialized &&
-                view.views.every(a => a.displayedRegions.length > 0 && a.initialized),
-        };
-    }, ({ initialized }) => {
-        if (!initialized) {
-            return;
-        }
-        const { level } = self;
-        const { assemblyManager } = (0, util_1.getSession)(self);
-        const view = (0, util_1.getContainingView)(self);
-        const viewSnaps = view.views.map(view => ({
-            ...(0, mobx_state_tree_1.getSnapshot)(view),
-            width: view.width,
-            staticBlocks: view.staticBlocks,
-            interRegionPaddingWidth: view.interRegionPaddingWidth,
-            minimumBlockWidth: view.minimumBlockWidth,
-        }));
-        const map = [];
-        const feats = self.features || [];
-        for (const f of feats) {
-            const mate = f.get('mate');
-            let f1s = f.get('start');
-            let f1e = f.get('end');
-            const f2s = mate.start;
-            const f2e = mate.end;
-            if (f.get('strand') === -1) {
-                ;
-                [f1e, f1s] = [f1s, f1e];
-            }
-            const a1 = assemblyManager.get(f.get('assemblyName'));
-            const a2 = assemblyManager.get(mate.assemblyName);
-            const r1 = f.get('refName');
-            const r2 = mate.refName;
-            const ref1 = (a1 === null || a1 === void 0 ? void 0 : a1.getCanonicalRefName(r1)) || r1;
-            const ref2 = (a2 === null || a2 === void 0 ? void 0 : a2.getCanonicalRefName(r2)) || r2;
-            const v1 = viewSnaps[level];
-            const v2 = viewSnaps[level + 1];
-            const p11 = (0, Base1DUtils_1.bpToPx)({ self: v1, refName: ref1, coord: f1s });
-            const p12 = (0, Base1DUtils_1.bpToPx)({ self: v1, refName: ref1, coord: f1e });
-            const p21 = (0, Base1DUtils_1.bpToPx)({ self: v2, refName: ref2, coord: f2s });
-            const p22 = (0, Base1DUtils_1.bpToPx)({ self: v2, refName: ref2, coord: f2e });
-            if (p11 === undefined ||
-                p12 === undefined ||
-                p21 === undefined ||
-                p22 === undefined) {
-                continue;
-            }
-            const cigar = f.get('CIGAR');
-            map.push({
-                p11,
-                p12,
-                p21,
-                p22,
-                f,
-                cigar: plugin_alignments_1.MismatchParser.parseCigar(cigar),
-            });
-        }
-        self.setFeatPositions(map);
-    }, { fireImmediately: true }));
-}