@jbrowse/plugin-dotplot-view 2.6.1

package/dist/DotplotView/model.js

@@ -0,0 +1,647 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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.Dotplot1DView = void 0;
+const react_1 = require("react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const file_saver_1 = require("file-saver");
+const mobx_1 = require("mobx");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const BaseViewModel_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/models/BaseViewModel"));
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+// icons
+const Icons_1 = require("@jbrowse/core/ui/Icons");
+const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
+const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
+// locals
+const _1dview_1 = require("./1dview");
+const util_2 = require("./components/util");
+// lazies
+const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
+const ReturnToImportFormDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ReturnToImportFormDialog'))));
+/**
+ * #stateModel DotplotView
+ * #category view
+ * extends  `BaseViewModel`
+ */
+function stateModelFactory(pm) {
+    return mobx_state_tree_1.types
+        .compose(BaseViewModel_1.default, mobx_state_tree_1.types.model('DotplotView', {
+        /**
+         * #property
+         */
+        id: mst_1.ElementId,
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('DotplotView'),
+        /**
+         * #property
+         */
+        height: 600,
+        /**
+         * #property
+         */
+        borderSize: 20,
+        /**
+         * #property
+         */
+        tickSize: 5,
+        /**
+         * #property
+         */
+        vtextRotation: 0,
+        /**
+         * #property
+         */
+        htextRotation: -90,
+        /**
+         * #property
+         */
+        fontSize: 15,
+        /**
+         * #property
+         */
+        trackSelectorType: 'hierarchical',
+        /**
+         * #property
+         */
+        assemblyNames: mobx_state_tree_1.types.array(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        drawCigar: true,
+        /**
+         * #property
+         */
+        hview: mobx_state_tree_1.types.optional(_1dview_1.DotplotHView, {}),
+        /**
+         * #property
+         */
+        vview: mobx_state_tree_1.types.optional(_1dview_1.DotplotVView, {}),
+        /**
+         * #property
+         */
+        tracks: mobx_state_tree_1.types.array(pm.pluggableMstType('track', 'stateModel')),
+        /**
+         * #property
+         * this represents tracks specific to this view specifically used
+         * for read vs ref dotplots where this track would not really apply
+         * elsewhere
+         */
+        viewTrackConfigs: mobx_state_tree_1.types.array(pm.pluggableConfigSchemaType('track')),
+    }))
+        .volatile(() => ({
+        volatileWidth: undefined,
+        volatileError: undefined,
+        // these are 'personal preferences', stored in volatile and
+        // loaded/written to localStorage
+        cursorMode: (0, util_1.localStorageGetItem)('dotplot-cursorMode') || 'crosshair',
+        showPanButtons: Boolean(JSON.parse((0, util_1.localStorageGetItem)('dotplot-showPanbuttons') || 'true')),
+        wheelMode: (0, util_1.localStorageGetItem)('dotplot-wheelMode') || 'zoom',
+        borderX: 100,
+        borderY: 100,
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get width() {
+            if (!self.volatileWidth) {
+                throw new Error('width not initialized');
+            }
+            return self.volatileWidth;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get assemblyErrors() {
+            const { assemblyManager } = (0, util_1.getSession)(self);
+            return self.assemblyNames
+                .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
+                .filter(f => !!f)
+                .join(', ');
+        },
+        /**
+         * #getter
+         */
+        get assembliesInitialized() {
+            const { assemblyManager } = (0, util_1.getSession)(self);
+            return self.assemblyNames.every(n => { var _a, _b; return (_b = (_a = assemblyManager.get(n)) === null || _a === void 0 ? void 0 : _a.initialized) !== null && _b !== void 0 ? _b : true; });
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get initialized() {
+            return (self.volatileWidth !== undefined &&
+                self.hview.displayedRegions.length > 0 &&
+                self.vview.displayedRegions.length > 0 &&
+                self.assembliesInitialized);
+        },
+        /**
+         * #getter
+         */
+        get hticks() {
+            const { hview } = self;
+            const { dynamicBlocks, staticBlocks, bpPerPx } = hview;
+            return dynamicBlocks.contentBlocks.length > 5
+                ? []
+                : (0, util_2.makeTicks)(staticBlocks.contentBlocks, bpPerPx);
+        },
+        /**
+         * #getter
+         */
+        get vticks() {
+            const { vview } = self;
+            const { dynamicBlocks, staticBlocks, bpPerPx } = vview;
+            return dynamicBlocks.contentBlocks.length > 5
+                ? []
+                : (0, util_2.makeTicks)(staticBlocks.contentBlocks, bpPerPx);
+        },
+        /**
+         * #getter
+         */
+        get loading() {
+            return self.assemblyNames.length > 0 && !this.initialized;
+        },
+        /**
+         * #getter
+         */
+        get viewWidth() {
+            return self.width - self.borderX;
+        },
+        /**
+         * #getter
+         */
+        get viewHeight() {
+            return self.height - self.borderY;
+        },
+        /**
+         * #getter
+         */
+        get views() {
+            return [self.hview, self.vview];
+        },
+        /**
+         * #method
+         */
+        renderProps() {
+            const session = (0, util_1.getSession)(self);
+            return {
+                ...(0, tracks_1.getParentRenderProps)(self),
+                drawCigar: self.drawCigar,
+                highResolutionScaling: (0, configuration_1.getConf)(session, 'highResolutionScaling'),
+            };
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setShowPanButtons(flag) {
+            self.showPanButtons = flag;
+        },
+        /**
+         * #action
+         */
+        setWheelMode(str) {
+            self.wheelMode = str;
+        },
+        /**
+         * #action
+         */
+        setCursorMode(str) {
+            self.cursorMode = str;
+        },
+        /**
+         * #action
+         */
+        setDrawCigar(flag) {
+            self.drawCigar = flag;
+        },
+        /**
+         * #action
+         * returns to the import form
+         */
+        clearView() {
+            self.hview.setDisplayedRegions([]);
+            self.vview.setDisplayedRegions([]);
+            self.assemblyNames = (0, mobx_state_tree_1.cast)([]);
+            self.tracks.clear();
+        },
+        /**
+         * #action
+         */
+        setBorderX(n) {
+            self.borderX = n;
+        },
+        /**
+         * #action
+         */
+        setBorderY(n) {
+            self.borderY = n;
+        },
+        /**
+         * #action
+         */
+        setWidth(newWidth) {
+            self.volatileWidth = newWidth;
+            return self.volatileWidth;
+        },
+        /**
+         * #action
+         */
+        setHeight(newHeight) {
+            self.height = newHeight;
+            return self.height;
+        },
+        /**
+         * #action
+         */
+        setError(e) {
+            self.volatileError = e;
+        },
+        /**
+         * #action
+         * removes the view itself from the state tree entirely by calling the
+         * parent removeView
+         */
+        closeView() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
+        },
+        /**
+         * #action
+         */
+        zoomOutButton() {
+            self.hview.zoomOut();
+            self.vview.zoomOut();
+        },
+        /**
+         * #action
+         */
+        zoomInButton() {
+            self.hview.zoomIn();
+            self.vview.zoomIn();
+        },
+        /**
+         * #action
+         */
+        activateTrackSelector() {
+            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 });
+                    session.showWidget(selector);
+                    return selector;
+                }
+            }
+            throw new Error(`invalid track selector type ${self.trackSelectorType}`);
+        },
+        /**
+         * #action
+         */
+        showTrack(trackId, initialSnapshot = {}) {
+            const schema = pm.pluggableConfigSchemaType('track');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
+            const trackType = pm.getTrackType(conf.type);
+            if (!trackType) {
+                throw new Error(`unknown track type ${conf.type}`);
+            }
+            const viewType = pm.getViewType(self.type);
+            const displayConf = conf.displays.find((d) => viewType.displayTypes.find(type => type.name === d.type));
+            if (!displayConf) {
+                throw new Error(`could not find a compatible display for view type ${self.type}`);
+            }
+            const track = trackType.stateModel.create({
+                ...initialSnapshot,
+                type: conf.type,
+                configuration: conf,
+                displays: [{ type: displayConf.type, configuration: displayConf }],
+            });
+            self.tracks.push(track);
+        },
+        /**
+         * #action
+         */
+        hideTrack(trackId) {
+            const schema = pm.pluggableConfigSchemaType('track');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
+            const t = self.tracks.filter(t => t.configuration === conf);
+            (0, mobx_1.transaction)(() => t.forEach(t => self.tracks.remove(t)));
+            return t.length;
+        },
+        /**
+         * #action
+         */
+        toggleTrack(trackId) {
+            const hiddenCount = this.hideTrack(trackId);
+            if (!hiddenCount) {
+                this.showTrack(trackId);
+            }
+        },
+        /**
+         * #action
+         */
+        setAssemblyNames(target, query) {
+            self.assemblyNames = (0, mobx_state_tree_1.cast)([target, query]);
+        },
+        /**
+         * #action
+         */
+        setViews(arr) {
+            self.hview = (0, mobx_state_tree_1.cast)(arr[0]);
+            self.vview = (0, mobx_state_tree_1.cast)(arr[1]);
+        },
+        /**
+         * #action
+         */
+        getCoords(mousedown, mouseup) {
+            const [xmin, xmax] = (0, util_1.minmax)(mouseup[0], mousedown[0]);
+            const [ymin, ymax] = (0, util_1.minmax)(mouseup[1], mousedown[1]);
+            return Math.abs(xmax - xmin) > 3 && Math.abs(ymax - ymin) > 3
+                ? [
+                    self.hview.pxToBp(xmin),
+                    self.hview.pxToBp(xmax),
+                    self.vview.pxToBp(self.viewHeight - ymin),
+                    self.vview.pxToBp(self.viewHeight - ymax),
+                ]
+                : undefined;
+        },
+        /**
+         * #action
+         * zooms into clicked and dragged region
+         */
+        zoomIn(mousedown, mouseup) {
+            const result = this.getCoords(mousedown, mouseup);
+            if (result) {
+                const [x1, x2, y1, y2] = result;
+                self.hview.moveTo(x1, x2);
+                self.vview.moveTo(y2, y1);
+            }
+        },
+        /**
+         * #action
+         */
+        showAllRegions() {
+            self.hview.zoomTo(self.hview.maxBpPerPx);
+            self.vview.zoomTo(self.vview.maxBpPerPx);
+            self.vview.center();
+            self.hview.center();
+        },
+        /**
+         * #action
+         * creates a linear synteny view from the clicked and dragged region
+         */
+        onDotplotView(mousedown, mouseup) {
+            const result = this.getCoords(mousedown, mouseup);
+            if (result) {
+                const [x1, x2, y1, y2] = result;
+                const session = (0, util_1.getSession)(self);
+                const d1 = _1dview_1.Dotplot1DView.create({
+                    ...(0, mobx_state_tree_1.getSnapshot)(self.hview),
+                    minimumBlockWidth: 0,
+                    interRegionPaddingWidth: 0,
+                });
+                const d2 = _1dview_1.Dotplot1DView.create({
+                    ...(0, mobx_state_tree_1.getSnapshot)(self.vview),
+                    minimumBlockWidth: 0,
+                    interRegionPaddingWidth: 0,
+                });
+                d1.setVolatileWidth(self.hview.width);
+                d2.setVolatileWidth(self.vview.width);
+                d1.moveTo(x1, x2);
+                d2.moveTo(y2, y1);
+                d1.zoomTo(d1.bpPerPx / (self.width / self.hview.width), 0);
+                d2.zoomTo(d2.bpPerPx / (self.width / self.vview.width), 0);
+                // add the specific evidence tracks to the LGVs in the split view
+                // note: scales the bpPerPx by scaling proportional of the dotplot
+                // width to the eventual lgv width
+                const tracks = self.tracks
+                    .map(track => track.configuration.displays.find((display) => display.type === 'LinearSyntenyDisplay'))
+                    .filter(f => !!f)
+                    .map(displayConf => {
+                    const trackConf = (0, mobx_state_tree_1.getParent)(displayConf, 2);
+                    return {
+                        type: trackConf.type,
+                        configuration: trackConf,
+                        displays: [
+                            { type: displayConf.type, configuration: displayConf },
+                        ],
+                    };
+                });
+                const { id: _unused1, ...rest1 } = (0, mobx_state_tree_1.getSnapshot)(d1);
+                const { id: _unused2, ...rest2 } = (0, mobx_state_tree_1.getSnapshot)(d2);
+                const viewSnapshot = {
+                    type: 'LinearSyntenyView',
+                    views: [
+                        {
+                            type: 'LinearGenomeView',
+                            tracks: [],
+                            hideHeader: true,
+                            ...rest1,
+                        },
+                        {
+                            type: 'LinearGenomeView',
+                            tracks: [],
+                            hideHeader: true,
+                            ...rest2,
+                        },
+                    ],
+                    tracks,
+                };
+                session.addView('LinearSyntenyView', viewSnapshot);
+            }
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         * creates an svg export and save using FileSaver
+         */
+        async exportSvg(opts = {}) {
+            const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGDotplotView')));
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
+        },
+        // if any of our assemblies are temporary assemblies
+        beforeDestroy() {
+            const session = (0, util_1.getSession)(self);
+            self.assemblyNames.forEach(asm => session.removeTemporaryAssembly(asm));
+        },
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                const s = (s) => JSON.stringify(s);
+                const { showPanButtons, wheelMode, cursorMode } = self;
+                if (typeof localStorage !== 'undefined') {
+                    localStorage.setItem('dotplot-showPanbuttons', s(showPanButtons));
+                    localStorage.setItem('dotplot-cursorMode', cursorMode);
+                    localStorage.setItem('dotplot-wheelMode', wheelMode);
+                }
+            }));
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                const session = (0, util_1.getSession)(self);
+                // don't operate if width not set yet
+                if (self.volatileWidth === undefined ||
+                    !self.assembliesInitialized) {
+                    return;
+                }
+                // also don't operate if displayedRegions already set, this is a
+                // helper autorun to load regions from assembly
+                if (self.hview.displayedRegions.length > 0 &&
+                    self.vview.displayedRegions.length > 0) {
+                    return;
+                }
+                const views = [self.hview, self.vview];
+                (0, mobx_1.transaction)(() => {
+                    self.assemblyNames.forEach((name, index) => {
+                        const assembly = session.assemblyManager.get(name);
+                        const view = views[index];
+                        view.setDisplayedRegions((assembly === null || assembly === void 0 ? void 0 : assembly.regions) || []);
+                    });
+                    self.showAllRegions();
+                });
+            }, { delay: 1000 }));
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(function borderSetter() {
+                // make sure we have a width on the view before trying to load
+                if (self.volatileWidth === undefined) {
+                    return;
+                }
+                const { vview, hview, viewHeight, viewWidth } = self;
+                const padding = 40;
+                const vblocks = vview.dynamicBlocks.contentBlocks;
+                const hblocks = hview.dynamicBlocks.contentBlocks;
+                const hoffset = hview.offsetPx;
+                const voffset = vview.offsetPx;
+                const vhide = (0, util_2.getBlockLabelKeysToHide)(vblocks, viewHeight, voffset);
+                const hhide = (0, util_2.getBlockLabelKeysToHide)(hblocks, viewWidth, hoffset);
+                const len = (a) => (0, util_1.measureText)(a.slice(0, 30));
+                const by = (0, util_1.max)(hblocks.filter(b => !hhide.has(b.key)).map(b => len(b.refName)));
+                const bx = (0, util_1.max)(vblocks.filter(b => !vhide.has(b.key)).map(b => len(b.refName)));
+                // these are set via autorun to avoid dependency cycle
+                self.setBorderY(Math.max(by + padding, 50));
+                self.setBorderX(Math.max(bx + padding, 50));
+            }));
+        },
+        /**
+         * #action
+         */
+        squareView() {
+            const { hview, vview } = self;
+            const avg = (hview.bpPerPx + vview.bpPerPx) / 2;
+            const hpx = hview.pxToBp(hview.width / 2);
+            const vpx = vview.pxToBp(vview.width / 2);
+            hview.setBpPerPx(avg);
+            hview.centerAt(hpx.coord, hpx.refName, hpx.index);
+            vview.setBpPerPx(avg);
+            vview.centerAt(vpx.coord, vpx.refName, vpx.index);
+        },
+        /**
+         * #action
+         */
+        squareViewProportional() {
+            const { hview, vview } = self;
+            const ratio = hview.width / vview.width;
+            const avg = (hview.bpPerPx + vview.bpPerPx) / 2;
+            const hpx = hview.pxToBp(hview.width / 2);
+            const vpx = vview.pxToBp(vview.width / 2);
+            hview.setBpPerPx(avg / ratio);
+            hview.centerAt(hpx.coord, hpx.refName, hpx.index);
+            vview.setBpPerPx(avg);
+            vview.centerAt(vpx.coord, vpx.refName, vpx.index);
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
+        menuItems() {
+            const session = (0, util_1.getSession)(self);
+            return [
+                {
+                    label: 'Return to import form',
+                    onClick: () => {
+                        (0, util_1.getSession)(self).queueDialog(handleClose => [
+                            ReturnToImportFormDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                    icon: FolderOpen_1.default,
+                },
+                {
+                    label: 'Square view - same bp per pixel',
+                    onClick: () => self.squareView(),
+                },
+                {
+                    label: 'Rectangular view - same total bp',
+                    onClick: () => self.squareView(),
+                },
+                {
+                    label: 'Show all regions',
+                    onClick: () => self.showAllRegions(),
+                },
+                {
+                    label: 'Export SVG',
+                    icon: PhotoCamera_1.default,
+                    onClick: () => {
+                        (0, util_1.getSession)(self).queueDialog(handleClose => [
+                            ExportSvgDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+                ...((0, util_1.isSessionModelWithWidgets)(session)
+                    ? [
+                        {
+                            label: 'Open track selector',
+                            onClick: self.activateTrackSelector,
+                            icon: Icons_1.TrackSelector,
+                        },
+                    ]
+                    : []),
+            ];
+        },
+        /**
+         * #getter
+         */
+        get error() {
+            return self.volatileError || self.assemblyErrors;
+        },
+    }));
+}
+exports.default = stateModelFactory;
+var _1dview_2 = require("./1dview");
+Object.defineProperty(exports, "Dotplot1DView", { enumerable: true, get: function () { return _1dview_2.Dotplot1DView; } });
+//# sourceMappingURL=model.js.map

package/dist/DotplotView/model.js.map

@@ -0,0 +1 @@
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package/dist/DotplotView/svgcomponents/SVGBackground.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+export default function SVGBackground({ width, height, }: {
+    width: number;
+    height: number;
+}): React.JSX.Element;