@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/esm/LinearReadArcsDisplay/model.js

@@ -0,0 +1,299 @@
+import React, { lazy } from 'react';
+import { autorun } from 'mobx';
+import { addDisposer, cast, types } from 'mobx-state-tree';
+import { ConfigurationReference, ConfigurationSchema, getConf, } from '@jbrowse/core/configuration';
+import { getSession, getContainingView } from '@jbrowse/core/util';
+import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
+// icons
+import PaletteIcon from '@mui/icons-material/Palette';
+import FilterListIcon from '@mui/icons-material/ClearAll';
+// locals
+import { FilterModel } from '../shared';
+import drawFeats from './drawFeats';
+import { fetchChains } from '../shared/fetchChains';
+// async
+const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
+/**
+ * #stateModel LinearReadArcsDisplay
+ * extends `BaseLinearDisplay`
+ */
+function stateModelFactory(configSchema) {
+    return types
+        .compose('LinearReadArcsDisplay', BaseLinearDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearReadArcsDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        filterBy: types.optional(FilterModel, {}),
+        /**
+         * #property
+         */
+        lineWidth: types.maybe(types.number),
+        /**
+         * #property
+         */
+        colorBy: types.maybe(types.model({
+            type: types.string,
+            tag: types.maybe(types.string),
+            extra: types.frozen(),
+        })),
+        /**
+         * #property
+         */
+        drawInter: true,
+        /**
+         * #property
+         */
+        drawLongRange: true,
+    }))
+        .volatile(() => ({
+        loading: false,
+        drawn: false,
+        chainData: undefined,
+        ref: null,
+        lastDrawnOffsetPx: 0,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         */
+        reload() {
+            self.error = undefined;
+        },
+        /**
+         * #action
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         */
+        setRef(ref) {
+            self.ref = ref;
+        },
+        /**
+         * #action
+         */
+        setColorScheme(s) {
+            self.colorBy = cast(s);
+        },
+        /**
+         * #action
+         */
+        setChainData(args) {
+            self.chainData = args;
+        },
+        /**
+         * #action
+         */
+        setDrawInter(f) {
+            self.drawInter = f;
+        },
+        /**
+         * #action
+         */
+        setDrawLongRange(f) {
+            self.drawLongRange = f;
+        },
+        /**
+         * #action
+         */
+        setLoading(f) {
+            self.loading = f;
+        },
+        /**
+         * #action
+         * used during tests to detect when we can complete a snapshot test
+         */
+        setDrawn(f) {
+            self.drawn = f;
+        },
+        /**
+         * #action
+         */
+        setFilterBy(filter) {
+            self.filterBy = cast(filter);
+        },
+        /**
+         * #action
+         * allows the drawing to slide around a little bit if it takes a long time to refresh
+         */
+        setLastDrawnOffsetPx(n) {
+            self.lastDrawnOffsetPx = n;
+        },
+        /**
+         * #action
+         * thin, bold, extrabold, etc
+         */
+        setLineWidth(n) {
+            self.lineWidth = n;
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #getter
+             */
+            get lineWidthSetting() {
+                var _a;
+                return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
+            },
+            /**
+             * #getter
+             */
+            get ready() {
+                return !!self.chainData;
+            },
+            // we don't use a server side renderer, but we need to provide this
+            // to avoid confusing the system currently
+            get rendererTypeName() {
+                return 'PileupRenderer';
+            },
+            // we don't use a server side renderer, so this fills in minimal
+            // info so as not to crash
+            renderProps() {
+                return {
+                    ...superRenderProps(),
+                    // never ready, we don't want to use server side render
+                    notReady: true,
+                    config: ConfigurationSchema('empty', {}).create(),
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Filter by',
+                        icon: FilterListIcon,
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                FilterByTagDlg,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Line width',
+                        subMenu: [
+                            {
+                                label: 'Thin',
+                                onClick: () => self.setLineWidth(1),
+                            },
+                            {
+                                label: 'Bold',
+                                onClick: () => self.setLineWidth(2),
+                            },
+                            {
+                                label: 'Extra bold',
+                                onClick: () => self.setLineWidth(5),
+                            },
+                        ],
+                    },
+                    {
+                        label: 'Draw inter-region vertical lines',
+                        type: 'checkbox',
+                        checked: self.drawInter,
+                        onClick: () => self.setDrawInter(!self.drawInter),
+                    },
+                    {
+                        label: 'Draw long range connections',
+                        type: 'checkbox',
+                        checked: self.drawLongRange,
+                        onClick: () => self.setDrawLongRange(!self.drawLongRange),
+                    },
+                    {
+                        label: 'Color scheme',
+                        icon: PaletteIcon,
+                        subMenu: [
+                            {
+                                label: 'Insert size ± 3σ and orientation',
+                                onClick: () => self.setColorScheme({ type: 'insertSizeAndOrientation' }),
+                            },
+                            {
+                                label: 'Insert size ± 3σ',
+                                onClick: () => self.setColorScheme({ type: 'insertSize' }),
+                            },
+                            {
+                                label: 'Orientation',
+                                onClick: () => self.setColorScheme({ type: 'orientation' }),
+                            },
+                            {
+                                label: 'Insert size gradient',
+                                onClick: () => self.setColorScheme({ type: 'gradient' }),
+                            },
+                        ],
+                    },
+                ];
+            },
+        };
+    })
+        .views(self => ({
+        /**
+         * #method
+         */
+        async renderSvg(opts) {
+            const view = getContainingView(self);
+            const width = view.dynamicBlocks.totalWidthPx;
+            const height = self.height;
+            let str;
+            if (opts.rasterizeLayers) {
+                const canvas = document.createElement('canvas');
+                canvas.width = width * 2;
+                canvas.height = height * 2;
+                const ctx = canvas.getContext('2d');
+                if (!ctx) {
+                    return;
+                }
+                ctx.scale(2, 2);
+                await drawFeats(self, ctx);
+                str = (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+            }
+            else {
+                // @ts-ignore
+                const C2S = await import('canvas2svg');
+                const ctx = new C2S.default(width, height);
+                await drawFeats(self, ctx);
+                str = (
+                // eslint-disable-next-line react/no-danger
+                React.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } }));
+            }
+            return React.createElement("g", null, str);
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(() => fetchChains(self), { delay: 1000 }));
+            addDisposer(self, autorun(async () => {
+                try {
+                    const canvas = self.ref;
+                    if (!canvas) {
+                        return;
+                    }
+                    const ctx = canvas.getContext('2d');
+                    if (!ctx) {
+                        return;
+                    }
+                    ctx.clearRect(0, 0, canvas.width, self.height * 2);
+                    ctx.resetTransform();
+                    ctx.scale(2, 2);
+                    await drawFeats(self, ctx);
+                    self.setDrawn(true);
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            }, { delay: 1000 }));
+        },
+    }));
+}
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LinearReadArcsDisplay/model.js.map

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package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { LinearReadCloudDisplayModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearReadCloudDisplayModel;
+}) => JSX.Element;
+export default _default;

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -0,0 +1,44 @@
+import React from 'react';
+import { isAlive } from 'mobx-state-tree';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { getContainingView } from '@jbrowse/core/util';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
+const useStyles = makeStyles()(theme => ({
+    loading: {
+        paddingLeft: '0.6em',
+        backgroundColor: theme.palette.action.disabledBackground,
+        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
+        height: '100%',
+        width: '100%',
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+const Cloud = observer(function ({ model, }) {
+    const view = getContainingView(model);
+    return (React.createElement("canvas", { "data-testid": `ReadCloud-display-${model.drawn}`, ref: ref => {
+            if (isAlive(model)) {
+                model.setRef(ref);
+            }
+        }, style: {
+            position: 'absolute',
+            left: -view.offsetPx + model.lastDrawnOffsetPx,
+            width: view.dynamicBlocks.totalWidthPx,
+            height: model.height,
+        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+});
+export default observer(function ({ model, }) {
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const err = model.error;
+    return err ? (React.createElement(BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (React.createElement("div", { className: classes.loading, style: {
+            width: view.dynamicBlocks.totalWidthPx,
+            height: 20,
+            position: 'absolute',
+            left: Math.max(0, -view.offsetPx),
+        } },
+        React.createElement(LoadingEllipses, { message: model.message }))) : (React.createElement(Cloud, { model: model }));
+});
+//# sourceMappingURL=ReactComponent.js.map

package/esm/LinearReadCloudDisplay/components/ReactComponent.js.map

@@ -0,0 +1 @@
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package/esm/LinearReadCloudDisplay/configSchema.d.ts

@@ -0,0 +1,6 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearReadCloudDisplay
+ */
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchemaF;

package/esm/LinearReadCloudDisplay/configSchema.js

@@ -0,0 +1,49 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
+import { types } from 'mobx-state-tree';
+/**
+ * #config LinearReadCloudDisplay
+ */
+function configSchemaF(pluginManager) {
+    return ConfigurationSchema('LinearReadCloudDisplay', {
+        /**
+         * #slot
+         */
+        maxFeatureScreenDensity: {
+            type: 'number',
+            description: 'maximum features per pixel that is displayed in the view',
+            defaultValue: 5,
+        },
+        /**
+         * #slot
+         */
+        featureHeight: {
+            type: 'number',
+            defaultValue: 7,
+        },
+        /**
+         * #slot
+         */
+        colorScheme: {
+            type: 'stringEnum',
+            model: types.enumeration('colorScheme', [
+                'strand',
+                'normal',
+                'insertSize',
+                'insertSizeAndOrientation',
+                'mappingQuality',
+                'tag',
+            ]),
+            description: 'color scheme to use',
+            defaultValue: 'normal',
+        },
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
+        explicitlyTyped: true,
+    });
+}
+export default configSchemaF;
+//# sourceMappingURL=configSchema.js.map

package/esm/LinearReadCloudDisplay/configSchema.js.map

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package/esm/LinearReadCloudDisplay/drawFeats.d.ts

@@ -0,0 +1,10 @@
+import { ChainData } from '../shared/fetchChains';
+export default function drawFeats(self: {
+    setLastDrawnOffsetPx: (n: number) => void;
+    setError: (e: unknown) => void;
+    colorBy?: {
+        type: string;
+    };
+    height: number;
+    chainData?: ChainData;
+}, ctx: CanvasRenderingContext2D): Promise<void>;

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -0,0 +1,156 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { getContainingView } from '@jbrowse/core/util';
+// locals
+import { getOrientationColor, getInsertSizeColor, getInsertSizeAndOrientationColor, } from '../shared/color';
+// avoid drawing negative width features for SVG exports
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+export default async function drawFeats(self, ctx) {
+    var _a;
+    const { chainData } = self;
+    if (!chainData) {
+        return;
+    }
+    const featureHeight = getConf(self, 'featureHeight');
+    const displayHeight = self.height;
+    const view = getContainingView(self);
+    self.setLastDrawnOffsetPx(view.offsetPx);
+    const { chains, stats } = chainData;
+    const coords = [];
+    for (let i = 0; i < chains.length; i++) {
+        const chain = chains[i];
+        // if we're looking at a paired read (flag 1) then assume it is just two
+        // reads (some small cases may defy this assumption such as secondary
+        // alignments but this may be uncommon)
+        if (chain[0].flags & 1 && chain.length > 1) {
+            const v0 = chain[0];
+            const v1 = chain[1];
+            const r1s = view.bpToPx({
+                refName: v0.refName,
+                coord: v0.start,
+            });
+            const r1e = view.bpToPx({
+                refName: v0.refName,
+                coord: v0.end,
+            });
+            const r2s = view.bpToPx({
+                refName: v1.refName,
+                coord: v1.start,
+            });
+            const r2e = view.bpToPx({
+                refName: v1.refName,
+                coord: v1.end,
+            });
+            let distance = 0;
+            if (r1s !== undefined &&
+                r1e !== undefined &&
+                r2s !== undefined &&
+                r2e !== undefined) {
+                if (v0.refName === v1.refName) {
+                    const s = Math.min(v0.start, v1.start);
+                    const e = Math.max(v0.end, v1.end);
+                    distance = Math.abs(e - s);
+                }
+                coords.push({
+                    r1s: r1s.offsetPx,
+                    r1e: r1e.offsetPx,
+                    r2s: r2s.offsetPx,
+                    r2e: r2e.offsetPx,
+                    v0,
+                    v1,
+                    distance,
+                });
+            }
+        }
+        else {
+            // if we're not looking at pairs, then it could be a multiply-split-long
+            // read, so traverse chain
+            for (let i = 1; i < chain.length; i++) {
+                const v0 = chain[i - 1];
+                const v1 = chain[i];
+                const r1s = view.bpToPx({
+                    refName: v0.refName,
+                    coord: v0.start,
+                });
+                const r1e = view.bpToPx({
+                    refName: v0.refName,
+                    coord: v0.end,
+                });
+                const r2s = view.bpToPx({
+                    refName: v1.refName,
+                    coord: v1.start,
+                });
+                const r2e = view.bpToPx({
+                    refName: v1.refName,
+                    coord: v1.end,
+                });
+                let distance = 0;
+                if (r1s !== undefined &&
+                    r1e !== undefined &&
+                    r2s !== undefined &&
+                    r2e !== undefined) {
+                    if (v0.refName === v1.refName) {
+                        const s = Math.min(v0.start, v1.start);
+                        const e = Math.max(v0.end, v1.end);
+                        distance = Math.abs(e - s);
+                    }
+                    coords.push({
+                        r1s: r1s.offsetPx,
+                        r1e: r1e.offsetPx,
+                        r2s: r2s.offsetPx,
+                        r2e: r2e.offsetPx,
+                        v0,
+                        v1,
+                        distance,
+                    });
+                }
+            }
+        }
+    }
+    let max = 0;
+    for (let i = 0; i < coords.length; i++) {
+        const { distance } = coords[i];
+        max = Math.max(max, distance);
+    }
+    const halfHeight = featureHeight / 2 - 0.5;
+    const scaler = (displayHeight - 20) / Math.log(max);
+    for (let i = 0; i < coords.length; i++) {
+        const { r1s, r1e, r2s, r2e, v0, v1, distance } = coords[i];
+        const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+        const top = Math.log(distance) * scaler;
+        ctx.fillStyle = 'black';
+        const w = r2s - r1e;
+        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx);
+        if (type === 'insertSizeAndOrientation') {
+            ctx.fillStyle = getInsertSizeAndOrientationColor(v0, v1, stats);
+        }
+        else if (type === 'orientation') {
+            ctx.fillStyle = getOrientationColor(v0);
+        }
+        else if (type === 'insertSize') {
+            ctx.fillStyle = getInsertSizeColor(v0, v1, stats) || 'grey';
+        }
+        else if (type === 'gradient') {
+            const s = Math.min(v0.start, v1.start);
+            const e = Math.max(v0.end, v1.end);
+            ctx.fillStyle = `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`;
+        }
+        const w1 = Math.max(r1e - r1s, 2);
+        const w2 = Math.max(r2e - r2s, 2);
+        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx);
+        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx);
+    }
+}
+//# sourceMappingURL=drawFeats.js.map

package/esm/LinearReadCloudDisplay/drawFeats.js.map

@@ -0,0 +1 @@
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package/esm/LinearReadCloudDisplay/index.d.ts

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

package/esm/LinearReadCloudDisplay/index.js

@@ -0,0 +1,21 @@
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+// locals
+import ReactComponent from './components/ReactComponent';
+import configSchemaF from './configSchema';
+import stateModelF from './model';
+export default function register(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaF(pluginManager);
+        return new DisplayType({
+            name: 'LinearReadCloudDisplay',
+            displayName: 'Read cloud display',
+            configSchema,
+            stateModel: stateModelF(configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
+            ReactComponent,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/LinearReadCloudDisplay/index.js.map

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