@jbrowse/plugin-linear-comparative-view 2.6.1

package/esm/LinearReadVsRef/LinearReadVsRef.js

@@ -0,0 +1,258 @@
+import React, { useEffect, useState } from 'react';
+import { Button, CircularProgress, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+import { makeStyles } from 'tss-react/mui';
+import { getConf } from '@jbrowse/core/configuration';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getSession, getContainingView, gatherOverlaps, } from '@jbrowse/core/util';
+// locals
+import { MismatchParser } from '@jbrowse/plugin-alignments';
+const { featurizeSA, getClip, getLength, getLengthSansClipping, getTag } = MismatchParser;
+const useStyles = makeStyles()({
+    root: {
+        width: 300,
+    },
+});
+export default function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
+    const { classes } = useStyles();
+    // window size stored as string, because it corresponds to a textfield which
+    // is parsed as number on submit
+    const [windowSizeText, setWindowSize] = useState('0');
+    const [error, setError] = useState();
+    const [primaryFeature, setPrimaryFeature] = useState();
+    const windowSize = +windowSizeText;
+    // we need to fetch the primary alignment if the selected feature is 2048.
+    // this should be the first in the list of the SA tag
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            setError(undefined);
+            try {
+                if (preFeature.get('flags') & 2048) {
+                    const SA = getTag(preFeature, 'SA') || '';
+                    const primaryAln = SA.split(';')[0];
+                    const [saRef, saStart] = primaryAln.split(',');
+                    const { rpcManager } = getSession(track);
+                    const adapterConfig = getConf(track, 'adapter');
+                    const sessionId = getRpcSessionId(track);
+                    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+                        adapterConfig,
+                        sessionId,
+                        regions: [
+                            {
+                                refName: saRef,
+                                start: +saStart - 1,
+                                end: +saStart,
+                            },
+                        ],
+                    }));
+                    const result = feats.find(f => f.get('name') === preFeature.get('name') &&
+                        !(f.get('flags') & 2048) &&
+                        !(f.get('flags') & 256));
+                    if (result) {
+                        setPrimaryFeature(result);
+                    }
+                    else {
+                        throw new Error('primary feature not found');
+                    }
+                }
+                else {
+                    setPrimaryFeature(preFeature);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [preFeature, track]);
+    function onSubmit() {
+        try {
+            if (!primaryFeature) {
+                return;
+            }
+            const feature = primaryFeature;
+            const session = getSession(track);
+            const view = getContainingView(track);
+            const cigar = feature.get('CIGAR');
+            const flags = feature.get('flags');
+            const origStrand = feature.get('strand');
+            const SA = getTag(feature, 'SA') || '';
+            const readName = feature.get('name');
+            const clipPos = getClip(cigar, 1);
+            const readAssembly = `${readName}_assembly_${Date.now()}`;
+            const [trackAssembly] = getConf(track, 'assemblyNames');
+            const assemblyNames = [trackAssembly, readAssembly];
+            const trackId = `track-${Date.now()}`;
+            const trackName = `${readName}_vs_${trackAssembly}`;
+            // get the canonical refname for the read because if the
+            // read.get('refName') is chr1 and the actual fasta refName is 1 then no
+            // tracks can be opened on the top panel of the linear read vs ref
+            const { assemblyManager } = session;
+            const assembly = assemblyManager.get(trackAssembly);
+            if (!assembly) {
+                throw new Error('assembly not found');
+            }
+            const suppAlns = featurizeSA(SA, feature.id(), origStrand, readName, true);
+            const feat = feature.toJSON();
+            feat.clipPos = clipPos;
+            feat.strand = 1;
+            feat.mate = {
+                refName: readName,
+                start: clipPos,
+                end: clipPos + getLengthSansClipping(cigar),
+            };
+            // if secondary alignment or supplementary, calculate length from SA[0]'s
+            // CIGAR which is the primary alignments. otherwise it is the primary
+            // alignment just use seq.length if primary alignment
+            const totalLength = flags & 2048 ? getLength(suppAlns[0].CIGAR) : getLength(cigar);
+            const features = [feat, ...suppAlns];
+            features.forEach((f, idx) => {
+                f.refName = (assembly === null || assembly === void 0 ? void 0 : assembly.getCanonicalRefName(f.refName)) || f.refName;
+                f.syntenyId = idx;
+                f.mate.syntenyId = idx;
+                f.mate.uniqueId = `${f.uniqueId}_mate`;
+            });
+            features.sort((a, b) => a.clipPos - b.clipPos);
+            const featSeq = feature.get('seq');
+            // the config feature store includes synthetic mate features
+            // mapped to the read assembly
+            const configFeatureStore = [...features, ...features.map(f => f.mate)];
+            const expand = 2 * windowSize;
+            const refLen = features.reduce((a, f) => a + f.end - f.start + expand, 0);
+            const seqTrackId = `${readName}_${Date.now()}`;
+            const sequenceTrackConf = getConf(assembly, 'sequence');
+            const lgvRegions = gatherOverlaps(features.map(f => ({
+                ...f,
+                start: Math.max(0, f.start - windowSize),
+                end: f.end + windowSize,
+                assemblyName: trackAssembly,
+            })));
+            session.addTemporaryAssembly({
+                name: `${readAssembly}`,
+                sequence: {
+                    type: 'ReferenceSequenceTrack',
+                    name: `Read sequence`,
+                    trackId: seqTrackId,
+                    assemblyNames: [readAssembly],
+                    adapter: {
+                        type: 'FromConfigSequenceAdapter',
+                        noAssemblyManager: true,
+                        features: [
+                            {
+                                start: 0,
+                                end: totalLength,
+                                seq: featSeq || '',
+                                refName: readName,
+                                uniqueId: `${Math.random()}`,
+                            },
+                        ],
+                    },
+                },
+            });
+            session.addView('LinearSyntenyView', {
+                type: 'LinearSyntenyView',
+                views: [
+                    {
+                        type: 'LinearGenomeView',
+                        hideHeader: true,
+                        offsetPx: 0,
+                        bpPerPx: refLen / view.width,
+                        displayedRegions: lgvRegions,
+                        tracks: [
+                            {
+                                id: `${Math.random()}`,
+                                type: 'ReferenceSequenceTrack',
+                                assemblyNames: [trackAssembly],
+                                configuration: sequenceTrackConf.trackId,
+                                displays: [
+                                    {
+                                        id: `${Math.random()}`,
+                                        type: 'LinearReferenceSequenceDisplay',
+                                        showReverse: true,
+                                        showTranslation: false,
+                                        height: 35,
+                                        configuration: `${seqTrackId}-LinearReferenceSequenceDisplay`,
+                                    },
+                                ],
+                            },
+                        ],
+                    },
+                    {
+                        type: 'LinearGenomeView',
+                        hideHeader: true,
+                        offsetPx: 0,
+                        bpPerPx: totalLength / view.width,
+                        displayedRegions: [
+                            {
+                                assemblyName: readAssembly,
+                                start: 0,
+                                end: totalLength,
+                                refName: readName,
+                            },
+                        ],
+                        tracks: [
+                            {
+                                id: `${Math.random()}`,
+                                type: 'ReferenceSequenceTrack',
+                                configuration: seqTrackId,
+                                displays: [
+                                    {
+                                        id: `${Math.random()}`,
+                                        type: 'LinearReferenceSequenceDisplay',
+                                        showReverse: true,
+                                        showTranslation: false,
+                                        height: 35,
+                                        configuration: `${seqTrackId}-LinearReferenceSequenceDisplay`,
+                                    },
+                                ],
+                            },
+                        ],
+                    },
+                ],
+                viewTrackConfigs: [
+                    {
+                        type: 'SyntenyTrack',
+                        assemblyNames,
+                        adapter: {
+                            type: 'FromConfigAdapter',
+                            features: configFeatureStore,
+                        },
+                        trackId,
+                        name: trackName,
+                    },
+                ],
+                tracks: [
+                    {
+                        configuration: trackId,
+                        type: 'SyntenyTrack',
+                        displays: [
+                            {
+                                type: 'LinearSyntenyDisplay',
+                                configuration: `${trackId}-LinearSyntenyDisplay`,
+                            },
+                        ],
+                    },
+                ],
+                displayName: `${readName} vs ${trackAssembly}`,
+            });
+            handleClose();
+        }
+        catch (e) {
+            console.error(e);
+            setError(e);
+        }
+    }
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set window size" },
+        React.createElement(DialogContent, null, error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : !primaryFeature ? (React.createElement("div", null,
+            React.createElement(Typography, null, "To accurately perform comparison we are fetching the primary alignment. Loading primary feature..."),
+            React.createElement(CircularProgress, null))) : (React.createElement("div", { className: classes.root },
+            primaryFeature.get('flags') & 256 ? (React.createElement(Typography, { style: { color: 'orange' } }, "Note: You selected a secondary alignment (which generally does not have SA tags or SEQ fields) so do a full reconstruction of the alignment")) : null,
+            React.createElement(Typography, null, "Show an extra window size around each part of the split alignment. Using a larger value can allow you to see more genomic context."),
+            React.createElement(TextField, { value: windowSize, onChange: event => setWindowSize(event.target.value), label: "Set window size" })))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
+            React.createElement(Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));
+}
+//# sourceMappingURL=LinearReadVsRef.js.map

package/esm/LinearReadVsRef/LinearReadVsRef.js.map

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

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

package/esm/LinearReadVsRef/index.js

@@ -0,0 +1,49 @@
+import { getSession, getContainingTrack } from '@jbrowse/core/util';
+// icons
+import AddIcon from '@mui/icons-material/Add';
+// locals
+import ReadVsRefDialog from './LinearReadVsRef';
+function isDisplay(elt) {
+    return elt.name === 'LinearPileupDisplay';
+}
+export default function (pm) {
+    pm.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
+        if (!isDisplay(pluggableElement)) {
+            return pluggableElement;
+        }
+        pluggableElement.stateModel = pluggableElement.stateModel.extend(self => {
+            const superContextMenuItems = self.contextMenuItems;
+            return {
+                views: {
+                    contextMenuItems() {
+                        const feature = self.contextMenuFeature;
+                        const track = getContainingTrack(self);
+                        return [
+                            ...superContextMenuItems(),
+                            ...(feature
+                                ? [
+                                    {
+                                        label: 'Linear read vs ref',
+                                        icon: AddIcon,
+                                        onClick: () => {
+                                            getSession(self).queueDialog(handleClose => [
+                                                ReadVsRefDialog,
+                                                {
+                                                    track,
+                                                    feature,
+                                                    handleClose,
+                                                },
+                                            ]);
+                                        },
+                                    },
+                                ]
+                                : []),
+                        ];
+                    },
+                },
+            };
+        });
+        return pluggableElement;
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/LinearReadVsRef/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReadVsRef/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AAEnE,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,qBAAqB,CAAA;AAC3C,CAAC;AAED,MAAM,CAAC,OAAO,WAAW,EAAiB;IACxC,EAAE,CAAC,mBAAmB,CACpB,6BAA6B,EAC7B,CAAC,gBAAsC,EAAE,EAAE;QACzC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,EAAE;YAChC,OAAO,gBAAgB,CAAA;SACxB;QACD,gBAAgB,CAAC,UAAU,GAAG,gBAAgB,CAAC,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE;YACtE,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;YACnD,OAAO;gBACL,KAAK,EAAE;oBACL,gBAAgB;wBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;wBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;wBACtC,OAAO;4BACL,GAAG,qBAAqB,EAAE;4BAC1B,GAAG,CAAC,OAAO;gCACT,CAAC,CAAC;oCACE;wCACE,KAAK,EAAE,oBAAoB;wCAC3B,IAAI,EAAE,OAAO;wCACb,OAAO,EAAE,GAAG,EAAE;4CACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gDAC1C,eAAe;gDACf;oDACE,KAAK;oDACL,OAAO;oDACP,WAAW;iDACZ;6CACF,CAAC,CAAA;wCACJ,CAAC;qCACF;iCACF;gCACH,CAAC,CAAC,EAAE,CAAC;yBACR,CAAA;oBACH,CAAC;iBACF;aACF,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,gBAAgB,CAAA;IACzB,CAAC,CACF,CAAA;AACH,CAAC"}

package/esm/LinearSyntenyDisplay/afterAttach.d.ts

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

package/esm/LinearSyntenyDisplay/afterAttach.js

@@ -0,0 +1,104 @@
+import { addDisposer, getSnapshot } from 'mobx-state-tree';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { bpToPx } from '@jbrowse/core/util/Base1DUtils';
+import { MismatchParser } from '@jbrowse/plugin-alignments';
+import { reaction, autorun } from 'mobx';
+import { drawMouseoverSynteny, drawRef } from './drawSynteny';
+export function doAfterAttach(self) {
+    addDisposer(self, autorun(() => {
+        var _a, _b;
+        const view = getContainingView(self);
+        if (!view.initialized) {
+            return;
+        }
+        const ctx1 = (_a = self.mainCanvas) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+        const ctx3 = (_b = self.cigarClickMapCanvas) === null || _b === void 0 ? void 0 : _b.getContext('2d');
+        if (!ctx1 || !ctx3) {
+            return;
+        }
+        const height = view.middleComparativeHeight;
+        const width = view.width;
+        ctx1.clearRect(0, 0, width, height);
+        ctx3.clearRect(0, 0, width, height);
+        drawRef(self, ctx1, ctx3);
+    }));
+    addDisposer(self, autorun(() => {
+        const view = getContainingView(self);
+        if (!view.initialized) {
+            return;
+        }
+        drawMouseoverSynteny(self);
+    }));
+    // this attempts to reduce recalculation of feature positions drawn by
+    // the synteny view
+    //
+    // uses a reaction to say "we know the positions don't change in any
+    // relevant way unless bpPerPx changes or displayedRegions changes"
+    addDisposer(self, reaction(() => {
+        const view = getContainingView(self);
+        return {
+            bpPerPx: view.views.map(v => v.bpPerPx),
+            // stringifying 'deeply' accesses the displayed regions, see
+            // issue #3456
+            displayedRegions: JSON.stringify(view.views.map(v => v.displayedRegions)),
+            features: self.features,
+            initialized: view.initialized,
+        };
+    }, ({ initialized }) => {
+        if (!initialized) {
+            return;
+        }
+        const { assemblyManager } = getSession(self);
+        const view = getContainingView(self);
+        const viewSnaps = view.views.map(view => ({
+            ...getSnapshot(view),
+            width: view.width,
+            staticBlocks: view.staticBlocks,
+            interRegionPaddingWidth: view.interRegionPaddingWidth,
+            minimumBlockWidth: view.minimumBlockWidth,
+        }));
+        const map = [];
+        const feats = self.features || [];
+        for (let i = 0; i < feats.length; i++) {
+            const f = feats[i];
+            const mate = f.get('mate');
+            let f1s = f.get('start');
+            let f1e = f.get('end');
+            const f2s = mate.start;
+            const f2e = mate.end;
+            if (f.get('strand') === -1) {
+                ;
+                [f1e, f1s] = [f1s, f1e];
+            }
+            const a1 = assemblyManager === null || assemblyManager === void 0 ? void 0 : assemblyManager.get(f.get('assemblyName'));
+            const a2 = assemblyManager === null || assemblyManager === void 0 ? void 0 : assemblyManager.get(mate.assemblyName);
+            const r1 = f.get('refName');
+            const r2 = mate.refName;
+            const ref1 = (a1 === null || a1 === void 0 ? void 0 : a1.getCanonicalRefName(r1)) || r1;
+            const ref2 = (a2 === null || a2 === void 0 ? void 0 : a2.getCanonicalRefName(r2)) || r2;
+            const v1 = viewSnaps[0];
+            const v2 = viewSnaps[1];
+            const p11 = bpToPx({ self: v1, refName: ref1, coord: f1s });
+            const p12 = bpToPx({ self: v1, refName: ref1, coord: f1e });
+            const p21 = bpToPx({ self: v2, refName: ref2, coord: f2s });
+            const p22 = bpToPx({ self: v2, refName: ref2, coord: f2e });
+            if (p11 === undefined ||
+                p12 === undefined ||
+                p21 === undefined ||
+                p22 === undefined) {
+                continue;
+            }
+            const cigar = f.get('CIGAR');
+            map.push({
+                p11,
+                p12,
+                p21,
+                p22,
+                f,
+                cigar: MismatchParser.parseCigar(cigar),
+            });
+        }
+        self.setFeatPositions(map);
+    }, { fireImmediately: true }));
+}
+//# sourceMappingURL=afterAttach.js.map

package/esm/LinearSyntenyDisplay/afterAttach.js.map

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package/esm/LinearSyntenyDisplay/components/Component.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { LinearSyntenyDisplayModel } from '../model';
+declare const ServerSideRenderedBlockContent: ({ model, }: {
+    model: LinearSyntenyDisplayModel;
+}) => React.JSX.Element;
+export default ServerSideRenderedBlockContent;

package/esm/LinearSyntenyDisplay/components/Component.js

@@ -0,0 +1,59 @@
+import React, { useEffect, useState } from 'react';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+// locals
+import LinearSyntenyRendering from './LinearSyntenyRendering';
+const useStyles = makeStyles()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            paddingLeft: '0.6em',
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            textAlign: 'center',
+        },
+        blockMessage: {
+            background: '#f1f1f1',
+            padding: 10,
+        },
+        blockError: {
+            background: '#f1f1f1',
+            padding: 10,
+            color: 'red',
+        },
+    };
+});
+function LoadingMessage() {
+    // only show the loading message after 300ms to prevent excessive flickering
+    const [shown, setShown] = useState(false);
+    const { classes } = useStyles();
+    useEffect(() => {
+        const timeout = setTimeout(() => setShown(true), 300);
+        return () => clearTimeout(timeout);
+    });
+    return shown ? (React.createElement("div", { className: classes.loading },
+        React.createElement(LoadingEllipses, null))) : null;
+}
+function BlockMessage({ messageText }) {
+    const { classes } = useStyles();
+    return React.createElement("div", { className: classes.blockMessage }, messageText);
+}
+function BlockError({ error }) {
+    const { classes } = useStyles();
+    return React.createElement("div", { className: classes.blockError }, `${error}`);
+}
+const ServerSideRenderedBlockContent = observer(function ({ model, }) {
+    if (model.error) {
+        return React.createElement(BlockError, { error: model.error });
+    }
+    if (model.message) {
+        return React.createElement(BlockMessage, { messageText: model.message });
+    }
+    if (!model.features) {
+        return React.createElement(LoadingMessage, null);
+    }
+    return React.createElement(LinearSyntenyRendering, { model: model });
+});
+export default ServerSideRenderedBlockContent;
+//# sourceMappingURL=Component.js.map

package/esm/LinearSyntenyDisplay/components/Component.js.map

@@ -0,0 +1 @@
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package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.d.ts

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