@jbrowse/plugin-dotplot-view 2.6.1

package/esm/DotplotView/model.js

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+import { lazy } from 'react';
+import { addDisposer, cast, getParent, getRoot, getSnapshot, resolveIdentifier, types, } from 'mobx-state-tree';
+import { saveAs } from 'file-saver';
+import { autorun, transaction } from 'mobx';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
+import { getSession, isSessionModelWithWidgets, minmax, measureText, max, localStorageGetItem, } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+// icons
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+import FolderOpenIcon from '@mui/icons-material/FolderOpen';
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
+// locals
+import { Dotplot1DView, DotplotHView, DotplotVView } from './1dview';
+import { getBlockLabelKeysToHide, makeTicks } from './components/util';
+// lazies
+const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
+const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
+/**
+ * #stateModel DotplotView
+ * #category view
+ * extends  `BaseViewModel`
+ */
+export default function stateModelFactory(pm) {
+    return types
+        .compose(BaseViewModel, types.model('DotplotView', {
+        /**
+         * #property
+         */
+        id: ElementId,
+        /**
+         * #property
+         */
+        type: 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: types.array(types.string),
+        /**
+         * #property
+         */
+        drawCigar: true,
+        /**
+         * #property
+         */
+        hview: types.optional(DotplotHView, {}),
+        /**
+         * #property
+         */
+        vview: types.optional(DotplotVView, {}),
+        /**
+         * #property
+         */
+        tracks: 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: types.array(pm.pluggableConfigSchemaType('track')),
+    }))
+        .volatile(() => ({
+        volatileWidth: undefined,
+        volatileError: undefined,
+        // these are 'personal preferences', stored in volatile and
+        // loaded/written to localStorage
+        cursorMode: localStorageGetItem('dotplot-cursorMode') || 'crosshair',
+        showPanButtons: Boolean(JSON.parse(localStorageGetItem('dotplot-showPanbuttons') || 'true')),
+        wheelMode: 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 } = 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 } = 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
+                ? []
+                : makeTicks(staticBlocks.contentBlocks, bpPerPx);
+        },
+        /**
+         * #getter
+         */
+        get vticks() {
+            const { vview } = self;
+            const { dynamicBlocks, staticBlocks, bpPerPx } = vview;
+            return dynamicBlocks.contentBlocks.length > 5
+                ? []
+                : 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 = getSession(self);
+            return {
+                ...getParentRenderProps(self),
+                drawCigar: self.drawCigar,
+                highResolutionScaling: 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 = 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
+            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 = getSession(self);
+                if (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 = resolveIdentifier(schema, 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 = resolveIdentifier(schema, getRoot(self), trackId);
+            const t = self.tracks.filter(t => t.configuration === conf);
+            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 = cast([target, query]);
+        },
+        /**
+         * #action
+         */
+        setViews(arr) {
+            self.hview = cast(arr[0]);
+            self.vview = cast(arr[1]);
+        },
+        /**
+         * #action
+         */
+        getCoords(mousedown, mouseup) {
+            const [xmin, xmax] = minmax(mouseup[0], mousedown[0]);
+            const [ymin, ymax] = 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 = getSession(self);
+                const d1 = Dotplot1DView.create({
+                    ...getSnapshot(self.hview),
+                    minimumBlockWidth: 0,
+                    interRegionPaddingWidth: 0,
+                });
+                const d2 = Dotplot1DView.create({
+                    ...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 = getParent(displayConf, 2);
+                    return {
+                        type: trackConf.type,
+                        configuration: trackConf,
+                        displays: [
+                            { type: displayConf.type, configuration: displayConf },
+                        ],
+                    };
+                });
+                const { id: _unused1, ...rest1 } = getSnapshot(d1);
+                const { id: _unused2, ...rest2 } = 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 import('./svgcomponents/SVGDotplotView');
+            const html = await renderToSvg(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            saveAs(blob, opts.filename || 'image.svg');
+        },
+        // if any of our assemblies are temporary assemblies
+        beforeDestroy() {
+            const session = getSession(self);
+            self.assemblyNames.forEach(asm => session.removeTemporaryAssembly(asm));
+        },
+        afterAttach() {
+            addDisposer(self, 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);
+                }
+            }));
+            addDisposer(self, autorun(() => {
+                const session = 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];
+                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 }));
+            addDisposer(self, 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 = getBlockLabelKeysToHide(vblocks, viewHeight, voffset);
+                const hhide = getBlockLabelKeysToHide(hblocks, viewWidth, hoffset);
+                const len = (a) => measureText(a.slice(0, 30));
+                const by = max(hblocks.filter(b => !hhide.has(b.key)).map(b => len(b.refName)));
+                const bx = 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 = getSession(self);
+            return [
+                {
+                    label: 'Return to import form',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            ReturnToImportFormDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                    icon: FolderOpenIcon,
+                },
+                {
+                    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: PhotoCameraIcon,
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            ExportSvgDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+                ...(isSessionModelWithWidgets(session)
+                    ? [
+                        {
+                            label: 'Open track selector',
+                            onClick: self.activateTrackSelector,
+                            icon: TrackSelectorIcon,
+                        },
+                    ]
+                    : []),
+            ];
+        },
+        /**
+         * #getter
+         */
+        get error() {
+            return self.volatileError || self.assemblyErrors;
+        },
+    }));
+}
+export { Dotplot1DView } from './1dview';
+//# sourceMappingURL=model.js.map

package/esm/DotplotView/model.js.map

@@ -0,0 +1 @@
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package/esm/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;

package/esm/DotplotView/svgcomponents/SVGBackground.js

@@ -0,0 +1,7 @@
+import React from 'react';
+import { useTheme } from '@mui/material';
+export default function SVGBackground({ width, height, }) {
+    const theme = useTheme();
+    return (React.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
+}
+//# sourceMappingURL=SVGBackground.js.map

package/esm/DotplotView/svgcomponents/SVGBackground.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/DotplotView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,GAIP;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,OAAO,CACL,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC"}

package/esm/DotplotView/svgcomponents/SVGDotplotView.d.ts

@@ -0,0 +1,2 @@
+import { DotplotViewModel, ExportSvgOptions } from '../model';
+export declare function renderToSvg(model: DotplotViewModel, opts: ExportSvgOptions): Promise<string>;