@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/LinearPileupDisplay/model.js

@@ -0,0 +1,576 @@
+import { lazy } from 'react';
+import { autorun, observable } from 'mobx';
+import { cast, types, addDisposer, getEnv } from 'mobx-state-tree';
+import copy from 'copy-to-clipboard';
+import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
+import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
+// icons
+import VisibilityIcon from '@mui/icons-material/Visibility';
+import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+import SortIcon from '@mui/icons-material/Sort';
+import PaletteIcon from '@mui/icons-material/Palette';
+import FilterListIcon from '@mui/icons-material/ClearAll';
+import LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb';
+import { getUniqueTagValues, getUniqueModificationValues } from '../shared';
+// async
+const ColorByTagDlg = lazy(() => import('./components/ColorByTag'));
+const FilterByTagDlg = lazy(() => import('./components/FilterByTag'));
+const SortByTagDlg = lazy(() => import('./components/SortByTag'));
+const SetFeatureHeightDlg = lazy(() => import('./components/SetFeatureHeight'));
+const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
+const ModificationsDlg = lazy(() => import('./components/ColorByModifications'));
+// using a map because it preserves order
+const rendererTypes = new Map([
+    ['pileup', 'PileupRenderer'],
+    ['svg', 'SvgFeatureRenderer'],
+]);
+const stateModelFactory = (configSchema) => types
+    .compose('LinearPileupDisplay', BaseLinearDisplay, types.model({
+    type: types.literal('LinearPileupDisplay'),
+    configuration: ConfigurationReference(configSchema),
+    showSoftClipping: false,
+    featureHeight: types.maybe(types.number),
+    noSpacing: types.maybe(types.boolean),
+    fadeLikelihood: types.maybe(types.boolean),
+    trackMaxHeight: types.maybe(types.number),
+    mismatchAlpha: types.maybe(types.boolean),
+    sortedBy: types.maybe(types.model({
+        type: types.string,
+        pos: types.number,
+        tag: types.maybe(types.string),
+        refName: types.string,
+        assemblyName: types.string,
+    })),
+    colorBy: types.maybe(types.model({
+        type: types.string,
+        tag: types.maybe(types.string),
+        extra: types.frozen(),
+    })),
+    filterBy: types.optional(types.model({
+        flagInclude: types.optional(types.number, 0),
+        flagExclude: types.optional(types.number, 1540),
+        readName: types.maybe(types.string),
+        tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
+    }), {}),
+}))
+    .volatile(() => ({
+    colorTagMap: observable.map({}),
+    modificationTagMap: observable.map({}),
+    featureUnderMouseVolatile: undefined,
+    ready: false,
+}))
+    .actions(self => ({
+    setReady(flag) {
+        self.ready = flag;
+    },
+    setMaxHeight(n) {
+        self.trackMaxHeight = n;
+    },
+    setFeatureHeight(n) {
+        self.featureHeight = n;
+    },
+    setNoSpacing(flag) {
+        self.noSpacing = flag;
+    },
+    setColorScheme(colorScheme) {
+        self.colorTagMap = observable.map({}); // clear existing mapping
+        self.colorBy = cast(colorScheme);
+        self.ready = false;
+    },
+    updateModificationColorMap(uniqueModifications) {
+        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
+        uniqueModifications.forEach(value => {
+            if (!self.modificationTagMap.has(value)) {
+                const totalKeys = [...self.modificationTagMap.keys()].length;
+                const newColor = colorPalette[totalKeys];
+                self.modificationTagMap.set(value, newColor);
+            }
+        });
+    },
+    updateColorTagMap(uniqueTag) {
+        // pale color scheme
+        // https://cran.r-project.org/web/packages/khroma/vignettes/tol.html
+        // e.g. "tol_light"
+        const colorPalette = [
+            '#BBCCEE',
+            'pink',
+            '#CCDDAA',
+            '#EEEEBB',
+            '#FFCCCC',
+            'lightblue',
+            'lightgreen',
+            'tan',
+            '#CCEEFF',
+            'lightsalmon',
+        ];
+        uniqueTag.forEach(value => {
+            if (!self.colorTagMap.has(value)) {
+                const totalKeys = [...self.colorTagMap.keys()].length;
+                const newColor = colorPalette[totalKeys];
+                self.colorTagMap.set(value, newColor);
+            }
+        });
+    },
+    setFeatureUnderMouse(feat) {
+        self.featureUnderMouseVolatile = feat;
+    },
+}))
+    .actions(self => ({
+    afterAttach() {
+        addDisposer(self, autorun(async () => {
+            try {
+                const { rpcManager } = getSession(self);
+                const view = getContainingView(self);
+                const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
+                const { staticBlocks, bpPerPx } = view;
+                if (!self.estimatedStatsReady) {
+                    return;
+                }
+                if (self.regionTooLarge) {
+                    return;
+                }
+                // continually generate the vc pairing, set and rerender if any
+                // new values seen
+                if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
+                    const uniqueTagSet = await getUniqueTagValues(self, colorBy, staticBlocks);
+                    self.updateColorTagMap(uniqueTagSet);
+                }
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    const adapter = getConf(parentTrack, ['adapter']);
+                    self.updateModificationColorMap(await getUniqueModificationValues(self, adapter, colorBy, staticBlocks));
+                }
+                if (sortedBy) {
+                    const { pos, refName, assemblyName } = sortedBy;
+                    // render just the sorted region first
+                    await self.rendererType.renderInClient(rpcManager, {
+                        assemblyName,
+                        regions: [
+                            {
+                                start: pos,
+                                end: pos + 1,
+                                refName,
+                                assemblyName,
+                            },
+                        ],
+                        adapterConfig: adapterConfig,
+                        rendererType: rendererType.name,
+                        sessionId: getRpcSessionId(self),
+                        layoutId: view.id,
+                        timeout: 1000000,
+                        ...self.renderProps(),
+                    });
+                    self.setReady(true);
+                    self.setCurrBpPerPx(bpPerPx);
+                }
+                else {
+                    self.setReady(true);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                self.setError(e);
+            }
+        }, { delay: 1000 }));
+        // autorun synchronizes featureUnderMouse with featureIdUnderMouse
+        addDisposer(self, autorun(async () => {
+            var _a;
+            const session = getSession(self);
+            try {
+                const featureId = self.featureIdUnderMouse;
+                if (((_a = self.featureUnderMouse) === null || _a === void 0 ? void 0 : _a.id()) !== featureId) {
+                    if (!featureId) {
+                        self.setFeatureUnderMouse(undefined);
+                    }
+                    else {
+                        const sessionId = getRpcSessionId(self);
+                        const view = getContainingView(self);
+                        const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                            featureId,
+                            sessionId,
+                            layoutId: view.id,
+                            rendererType: 'PileupRenderer',
+                        }));
+                        // check featureIdUnderMouse is still the same as the
+                        // feature.id that was returned e.g. that the user hasn't
+                        // moused over to a new position during the async operation
+                        // above
+                        // @ts-ignore
+                        if (self.featureIdUnderMouse === feature.uniqueId) {
+                            // @ts-ignore
+                            self.setFeatureUnderMouse(new SimpleFeature(feature));
+                        }
+                    }
+                }
+            }
+            catch (e) {
+                console.error(e);
+                session.notify(`${e}`, 'error');
+            }
+        }));
+    },
+    selectFeature(feature) {
+        const session = getSession(self);
+        if (isSessionModelWithWidgets(session)) {
+            const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', { featureData: feature.toJSON(), view: getContainingView(self) });
+            session.showWidget(featureWidget);
+        }
+        session.setSelection(feature);
+    },
+    clearSelected() {
+        self.sortedBy = undefined;
+    },
+    // uses copy-to-clipboard and generates notification
+    copyFeatureToClipboard(feature) {
+        const { uniqueId, ...rest } = feature.toJSON();
+        const session = getSession(self);
+        copy(JSON.stringify(rest, null, 4));
+        session.notify('Copied to clipboard', 'success');
+    },
+    toggleSoftClipping() {
+        self.showSoftClipping = !self.showSoftClipping;
+    },
+    toggleMismatchAlpha() {
+        self.mismatchAlpha = !self.mismatchAlpha;
+    },
+    setConfig(configuration) {
+        self.configuration = configuration;
+    },
+    setSortedBy(type, tag) {
+        const { centerLineInfo } = getContainingView(self);
+        if (!centerLineInfo) {
+            return;
+        }
+        const { refName, assemblyName, offset } = centerLineInfo;
+        const centerBp = Math.round(offset) + 1;
+        if (centerBp < 0 || !refName) {
+            return;
+        }
+        self.sortedBy = {
+            type,
+            pos: centerBp,
+            refName,
+            assemblyName,
+            tag,
+        };
+        self.ready = false;
+    },
+    setFilterBy(filter) {
+        self.filterBy = cast(filter);
+    },
+}))
+    .actions(self => {
+    // resets the sort object and refresh whole display on reload
+    const superReload = self.reload;
+    return {
+        reload() {
+            self.clearSelected();
+            superReload();
+        },
+    };
+})
+    .views(self => ({
+    get maxHeight() {
+        const conf = getConf(self, ['renderers', self.rendererTypeName]) || {};
+        return self.trackMaxHeight !== undefined
+            ? self.trackMaxHeight
+            : conf.maxHeight;
+    },
+    get rendererConfig() {
+        const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
+        return self.rendererType.configSchema.create({
+            ...configBlob,
+            height: self.featureHeight,
+            noSpacing: self.noSpacing,
+            maxHeight: this.maxHeight,
+            mismatchAlpha: self.mismatchAlpha,
+        }, getEnv(self));
+    },
+    get featureHeightSetting() {
+        return (self.featureHeight || readConfObject(this.rendererConfig, 'height'));
+    },
+    get mismatchAlphaSetting() {
+        return self.mismatchAlpha !== undefined
+            ? self.mismatchAlpha
+            : readConfObject(this.rendererConfig, 'mismatchAlpha');
+    },
+    get featureUnderMouse() {
+        return self.featureUnderMouseVolatile;
+    },
+}))
+    .views(self => {
+    const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+    return {
+        get rendererTypeName() {
+            const viewName = getConf(self, 'defaultRendering');
+            const rendererType = rendererTypes.get(viewName);
+            if (!rendererType) {
+                throw new Error(`unknown alignments view name ${viewName}`);
+            }
+            return rendererType;
+        },
+        contextMenuItems() {
+            const feat = self.contextMenuFeature;
+            const contextMenuItems = feat
+                ? [
+                    {
+                        label: 'Open feature details',
+                        icon: MenuOpenIcon,
+                        onClick: () => {
+                            self.clearFeatureSelection();
+                            if (feat) {
+                                self.selectFeature(feat);
+                            }
+                        },
+                    },
+                    {
+                        label: 'Copy info to clipboard',
+                        icon: ContentCopyIcon,
+                        onClick: () => {
+                            if (feat) {
+                                self.copyFeatureToClipboard(feat);
+                            }
+                        },
+                    },
+                ]
+                : [];
+            return contextMenuItems;
+        },
+        get DisplayBlurb() {
+            return LinearPileupDisplayBlurb;
+        },
+        renderProps() {
+            const view = getContainingView(self);
+            const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currBpPerPx, ready, } = self;
+            const superProps = superRenderProps();
+            return {
+                ...superProps,
+                notReady: superProps.notReady ||
+                    !ready ||
+                    (sortedBy && currBpPerPx !== view.bpPerPx),
+                rpcDriverName,
+                displayModel: self,
+                sortedBy,
+                colorBy,
+                filterBy: JSON.parse(JSON.stringify(filterBy)),
+                colorTagMap: Object.fromEntries(colorTagMap.toJSON()),
+                modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
+                showSoftClip: self.showSoftClipping,
+                config: self.rendererConfig,
+                async onFeatureClick(_, featureId) {
+                    const session = getSession(self);
+                    const { rpcManager } = session;
+                    try {
+                        const f = featureId || self.featureIdUnderMouse;
+                        if (!f) {
+                            self.clearFeatureSelection();
+                        }
+                        else {
+                            const sessionId = getRpcSessionId(self);
+                            const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                                featureId: f,
+                                sessionId,
+                                layoutId: getContainingView(self).id,
+                                rendererType: 'PileupRenderer',
+                            }));
+                            if (feature) {
+                                // @ts-ignore
+                                self.selectFeature(new SimpleFeature(feature));
+                            }
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                },
+                onClick() {
+                    self.clearFeatureSelection();
+                },
+                // similar to click but opens a menu with further options
+                async onFeatureContextMenu(_, featureId) {
+                    const session = getSession(self);
+                    const { rpcManager } = session;
+                    try {
+                        const f = featureId || self.featureIdUnderMouse;
+                        if (!f) {
+                            self.clearFeatureSelection();
+                        }
+                        else {
+                            const sessionId = getRpcSessionId(self);
+                            const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                                featureId: f,
+                                sessionId,
+                                layoutId: getContainingView(self).id,
+                                rendererType: 'PileupRenderer',
+                            }));
+                            if (feature) {
+                                // @ts-ignore
+                                self.setContextMenuFeature(new SimpleFeature(feature));
+                            }
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                },
+            };
+        },
+        trackMenuItems() {
+            return [
+                ...superTrackMenuItems(),
+                {
+                    label: 'Show soft clipping',
+                    icon: VisibilityIcon,
+                    type: 'checkbox',
+                    checked: self.showSoftClipping,
+                    onClick: () => {
+                        self.toggleSoftClipping();
+                        // if toggling from off to on, will break sort for this track
+                        // so clear it
+                        if (self.showSoftClipping) {
+                            self.clearSelected();
+                        }
+                    },
+                },
+                {
+                    label: 'Sort by',
+                    icon: SortIcon,
+                    disabled: self.showSoftClipping,
+                    subMenu: [
+                        ...['Start location', 'Read strand', 'Base pair'].map(option => ({
+                            label: option,
+                            onClick: () => self.setSortedBy(option),
+                        })),
+                        {
+                            label: 'Sort by tag...',
+                            onClick: () => {
+                                getSession(self).queueDialog(handleClose => [
+                                    SortByTagDlg,
+                                    { model: self, handleClose },
+                                ]);
+                            },
+                        },
+                        {
+                            label: 'Clear sort',
+                            onClick: () => self.clearSelected(),
+                        },
+                    ],
+                },
+                {
+                    label: 'Color scheme',
+                    icon: PaletteIcon,
+                    subMenu: [
+                        {
+                            label: 'Normal',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'normal' });
+                            },
+                        },
+                        {
+                            label: 'Mapping quality',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'mappingQuality' });
+                            },
+                        },
+                        {
+                            label: 'Strand',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'strand' });
+                            },
+                        },
+                        {
+                            label: 'Pair orientation',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'pairOrientation' });
+                            },
+                        },
+                        {
+                            label: 'Per-base quality',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'perBaseQuality' });
+                            },
+                        },
+                        {
+                            label: 'Per-base lettering',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'perBaseLettering' });
+                            },
+                        },
+                        {
+                            label: 'Modifications or methylation',
+                            onClick: () => {
+                                getSession(self).queueDialog(doneCallback => [
+                                    ModificationsDlg,
+                                    { model: self, handleClose: doneCallback },
+                                ]);
+                            },
+                        },
+                        {
+                            label: 'Insert size',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'insertSize' });
+                            },
+                        },
+                        {
+                            label: 'Stranded paired-end',
+                            onClick: () => {
+                                self.setColorScheme({ type: 'reverseTemplate' });
+                            },
+                        },
+                        {
+                            label: 'Color by tag...',
+                            onClick: () => {
+                                getSession(self).queueDialog(doneCallback => [
+                                    ColorByTagDlg,
+                                    { model: self, handleClose: doneCallback },
+                                ]);
+                            },
+                        },
+                    ],
+                },
+                {
+                    label: 'Filter by',
+                    icon: FilterListIcon,
+                    onClick: () => {
+                        getSession(self).queueDialog(doneCallback => [
+                            FilterByTagDlg,
+                            { model: self, handleClose: doneCallback },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Set feature height',
+                    onClick: () => {
+                        getSession(self).queueDialog(doneCallback => [
+                            SetFeatureHeightDlg,
+                            { model: self, handleClose: doneCallback },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Set max height',
+                    onClick: () => {
+                        getSession(self).queueDialog(doneCallback => [
+                            SetMaxHeightDlg,
+                            { model: self, handleClose: doneCallback },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Fade mismatches by quality',
+                    type: 'checkbox',
+                    checked: self.mismatchAlphaSetting,
+                    onClick: () => {
+                        self.toggleMismatchAlpha();
+                    },
+                },
+            ];
+        },
+    };
+});
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LinearPileupDisplay/model.js.map

@@ -0,0 +1 @@
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package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+declare type Coord = [number, number];
+declare const SNPCoverageTooltip: (props: {
+    model: any;
+    height: number;
+    offsetMouseCoord: Coord;
+    clientMouseCoord: Coord;
+    clientRect?: DOMRect;
+}) => JSX.Element | null;
+export default SNPCoverageTooltip;

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -0,0 +1,57 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { observer } from 'mobx-react';
+import { Tooltip } from '@jbrowse/plugin-wiggle';
+const en = (n) => n.toLocaleString('en-US');
+const toP = (s = 0) => +(+s).toFixed(1);
+const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
+const TooltipContents = React.forwardRef(({ feature }, reactRef) => {
+    const start = feature.get('start');
+    const end = feature.get('end');
+    const name = feature.get('refName');
+    const { refbase, all, total, ref, '-1': rn1, '1': r1, '0': r0, ...info } = feature.get('snpinfo');
+    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
+        .filter(f => !!f)
+        .join(':');
+    return (React.createElement("div", { ref: reactRef },
+        React.createElement("table", null,
+            React.createElement("caption", null, loc),
+            React.createElement("thead", null,
+                React.createElement("tr", null,
+                    React.createElement("th", null, "Base"),
+                    React.createElement("th", null, "Count"),
+                    React.createElement("th", null, "% of Total"),
+                    React.createElement("th", null, "Strands"),
+                    React.createElement("th", null, "Source"))),
+            React.createElement("tbody", null,
+                React.createElement("tr", null,
+                    React.createElement("td", null, "Total"),
+                    React.createElement("td", null, all)),
+                React.createElement("tr", null,
+                    React.createElement("td", null,
+                        "REF ",
+                        refbase ? `(${refbase.toUpperCase()})` : ''),
+                    React.createElement("td", null, ref),
+                    React.createElement("td", null, pct(ref, all)),
+                    React.createElement("td", null,
+                        rn1 ? `${rn1}(-)` : '',
+                        r1 ? `${r1}(+)` : ''),
+                    React.createElement("td", null)),
+                Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (React.createElement("tr", { key: base },
+                    React.createElement("td", null, base.toUpperCase()),
+                    React.createElement("td", null, score.total),
+                    React.createElement("td", null, base === 'total' || base === 'skip'
+                        ? '---'
+                        : pct(score.total, all)),
+                    React.createElement("td", null,
+                        score['-1'] ? `${score['-1']}(-)` : '',
+                        score['1'] ? `${score['1']}(+)` : ''),
+                    React.createElement("td", null, key)))))))));
+});
+const SNPCoverageTooltip = observer((props) => {
+    const { model } = props;
+    const { featureUnderMouse: feat } = model;
+    return feat && feat.get('type') === 'skip' ? null : (React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props }));
+});
+export default SNPCoverageTooltip;
+//# sourceMappingURL=Tooltip.js.map