jbrowse-plugin-msaview 1.0.17 → 2.0.0

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -0,0 +1,90 @@
+import React, { useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
+import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { makeStyles } from 'tss-react/mui';
+// locals
+import { getTranscriptDisplayName, getId, getTranscriptFeatures, } from '../../util';
+import { fetchGeneList } from './fetchGeneList';
+import { preCalculatedLaunchView } from './preCalculatedLaunchView';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+});
+const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
+    const session = getSession(model);
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const [error, setError] = useState();
+    const [geneNameList, setGeneNameList] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const data = await fetchGeneList();
+                setGeneNameList(data);
+                const set = new Set(data);
+                const options = getTranscriptFeatures(feature);
+                const ret = options.find(val => set.has(getId(val)));
+                if (ret) {
+                    setUserSelection(getId(ret));
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [feature]);
+    const set = new Set(geneNameList);
+    const options = getTranscriptFeatures(feature);
+    const ret = options.find(val => set.has(getId(val)));
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            React.createElement(Typography, null,
+                "The source data for these multiple sequence alignments is from",
+                ' ',
+                React.createElement("a", { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
+            geneNameList && !ret ? (React.createElement("div", { style: { color: 'red' } }, "No MSA data for this gene found")) : null,
+            React.createElement(TextField, { value: userSelection, onChange: event => setUserSelection(event.target.value), label: "Choose isoform to view MSA for", select: true },
+                options
+                    .filter(val => set.has(getId(val)))
+                    .map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
+                    getTranscriptDisplayName(val),
+                    " (has data)"))),
+                options
+                    .filter(val => !set.has(getId(val)))
+                    .map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: true }, getTranscriptDisplayName(val)))))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            if (!ret) {
+                                return;
+                            }
+                            await preCalculatedLaunchView({
+                                userSelection,
+                                session,
+                                newViewTitle: '',
+                                view,
+                                feature: ret,
+                            });
+                            handleClose();
+                        }
+                        catch (e) {
+                            console.error(e);
+                            setError(e);
+                        }
+                    })();
+                } }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => handleClose() }, "Cancel"))));
+});
+export default PreLoadedMSA;
+//# sourceMappingURL=PreLoadedMSADataPanel.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.d.ts

@@ -0,0 +1 @@
+export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.js

@@ -0,0 +1,12 @@
+export async function fetchGeneList() {
+    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
+    }
+    const result = await res.text();
+    return result
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f);
+}
+//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts

@@ -0,0 +1,9 @@
+import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }: {
+    session: AbstractSessionModel;
+    userSelection: string;
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    feature: Feature;
+}): Promise<void>;

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js

@@ -0,0 +1,36 @@
+import { ungzip } from 'pako';
+async function myfetch(url) {
+    const res = await fetch(url);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} fetching ${await res.text()}`);
+    }
+    const data = await res.arrayBuffer();
+    return new TextDecoder().decode(ungzip(data));
+}
+export async function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }) {
+    const d = await myfetch(`https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`);
+    session.addView('MsaView', {
+        type: 'MsaView',
+        displayName: newViewTitle,
+        treeAreaWidth: 200,
+        treeWidth: 100,
+        drawNodeBubbles: false,
+        labelsAlignRight: true,
+        showBranchLen: false,
+        colWidth: 10,
+        rowHeight: 12,
+        colorSchemeName: 'percent_identity_dynamic',
+        treeFilehandle: {
+            uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh',
+        },
+        treeMetadataFilehandle: {
+            uri: 'https://s3.amazonaws.com/jbrowse.org/demos/app/species.json',
+        },
+        data: {
+            msa: d,
+        },
+        connectedViewId: view.id,
+        connectedFeature: feature.toJSON(),
+    });
+}
+//# sourceMappingURL=preCalculatedLaunchView.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/TabUtils.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+interface TabPanelProps {
+    children?: React.ReactNode;
+    index: number;
+    value: number;
+}
+export declare function CustomTabPanel(props: TabPanelProps): React.JSX.Element;
+export declare function a11yProps(index: number): {
+    id: string;
+    'aria-controls': string;
+};
+export {};

package/dist/LaunchMsaView/components/TabUtils.js

@@ -0,0 +1,13 @@
+import React from 'react';
+import { Box } from '@mui/material';
+export function CustomTabPanel(props) {
+    const { children, value, index, ...other } = props;
+    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, id: `gtabpanel-${index}`, "aria-labelledby": `gtab-${index}`, ...other }, value === index && React.createElement(Box, { sx: { p: 3 } }, children)));
+}
+export function a11yProps(index) {
+    return {
+        id: `gtab-${index}`,
+        'aria-controls': `gtabpanel-${index}`,
+    };
+}
+//# sourceMappingURL=TabUtils.js.map

package/dist/LaunchMsaView/components/TabUtils.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/index.d.ts

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

package/dist/LaunchMsaView/index.js

@@ -0,0 +1,50 @@
+import { getSession, getContainingTrack } from '@jbrowse/core/util';
+// icons
+import AddIcon from '@mui/icons-material/Add';
+// locals
+import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
+function isDisplay(elt) {
+    return elt.name === 'LinearBasicDisplay';
+}
+function extendStateModel(stateModel) {
+    return stateModel.views(self => {
+        const superContextMenuItems = self.contextMenuItems;
+        return {
+            contextMenuItems() {
+                const feature = self.contextMenuFeature;
+                const track = getContainingTrack(self);
+                return [
+                    ...superContextMenuItems(),
+                    ...(feature
+                        ? [
+                            {
+                                label: 'Launch MSA view',
+                                icon: AddIcon,
+                                onClick: () => {
+                                    const session = getSession(track);
+                                    session.queueDialog(handleClose => [
+                                        LaunchMsaViewDialog,
+                                        {
+                                            model: track,
+                                            handleClose,
+                                            feature,
+                                        },
+                                    ]);
+                                },
+                            },
+                        ]
+                        : []),
+                ];
+            },
+        };
+    });
+}
+export default function LaunchMsaViewF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-extendPluggableElement', (elt) => {
+        if (isDisplay(elt)) {
+            elt.stateModel = extendStateModel(elt.stateModel);
+        }
+        return elt;
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/index.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/util.d.ts

@@ -0,0 +1,5 @@
+import { Feature } from '@jbrowse/core/util';
+export declare function getTranscriptFeatures(feature: Feature): Feature[];
+export declare function getId(val?: Feature): any;
+export declare function getTranscriptDisplayName(val?: Feature): string;
+export declare function getGeneDisplayName(val?: Feature): string;

package/dist/LaunchMsaView/util.js

@@ -0,0 +1,25 @@
+export function getTranscriptFeatures(feature) {
+    // check if we are looking at a 'two-level' or 'three-level' feature by
+    // finding exon/CDS subfeatures. we want to select from transcript names
+    const subfeatures = feature.get('subfeatures') ?? [];
+    return subfeatures.some(f => f.get('type') === 'CDS')
+        ? [feature]
+        : // filter out non-coding by finding subfeatures with CDS subfeatures
+            subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
+}
+export function getId(val) {
+    return val === undefined ? '' : val.get('name') || val.get('id');
+}
+export function getTranscriptDisplayName(val) {
+    return val === undefined
+        ? ''
+        : [val.get('name'), val.get('id')].filter(f => !!f).join(' ');
+}
+export function getGeneDisplayName(val) {
+    return val === undefined
+        ? ''
+        : [val.get('gene_name') || val.get('name'), val.get('id')]
+            .filter(f => !!f)
+            .join(' ');
+}
+//# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/util.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/components/LoadingBLAST.d.ts

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

package/dist/MsaViewPanel/components/LoadingBLAST.js

@@ -0,0 +1,36 @@
+import React from 'react';
+import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+// locals
+import RIDLink from './RIDLink';
+const useStyles = makeStyles()(theme => ({
+    margin: {
+        padding: 20,
+    },
+    loading: {
+        background: theme.palette.background.paper,
+    },
+}));
+function RIDError({ rid, error }) {
+    return (React.createElement("div", null,
+        rid ? React.createElement(RIDLink, { rid: rid }) : null,
+        React.createElement(ErrorMessage, { error: error })));
+}
+function RIDProgress({ rid, progress }) {
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.loading },
+        rid ? React.createElement(RIDLink, { rid: rid }) : null,
+        React.createElement(Typography, null, progress)));
+}
+const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
+    const { progress, rid, error, processing } = model;
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.margin },
+        React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
+        error ? (React.createElement(RIDError, { rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { rid: rid, progress: progress })) : null,
+        React.createElement(Typography, null, processing || 'Initializing BLAST query')));
+});
+export default LoadingBLAST;
+//# sourceMappingURL=LoadingBLAST.js.map

package/dist/MsaViewPanel/components/LoadingBLAST.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/components/MsaViewPanel.d.ts

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

package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -0,0 +1,10 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { MSAView } from 'react-msaview';
+import LoadingBLAST from './LoadingBLAST';
+const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
+    const { blastParams } = model;
+    return (React.createElement("div", null, blastParams ? React.createElement(LoadingBLAST, { model: model }) : React.createElement(MSAView, { model: model })));
+});
+export default MsaViewPanel;
+//# sourceMappingURL=MsaViewPanel.js.map

package/dist/MsaViewPanel/components/MsaViewPanel.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/components/RIDLink.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+declare function RIDLink({ rid }: {
+    rid: string;
+}): React.JSX.Element;
+export default RIDLink;

package/dist/MsaViewPanel/components/RIDLink.js

@@ -0,0 +1,17 @@
+import React from 'react';
+import { Link, Typography } from '@mui/material';
+// locals
+import OpenInNewIcon from '../../OpenInNewIcon';
+import { BLAST_URL } from '../../utils/ncbiBlast';
+function RIDLink({ rid }) {
+    return (React.createElement(Typography, null,
+        "RID ",
+        rid,
+        ' ',
+        React.createElement(Link, { target: "_black", href: `${BLAST_URL}?CMD=Get&RID=${rid}` },
+            "(see status at NCBI ",
+            React.createElement(OpenInNewIcon, null),
+            ")")));
+}
+export default RIDLink;
+//# sourceMappingURL=RIDLink.js.map

package/dist/MsaViewPanel/components/RIDLink.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/doLaunchBlast.d.ts

@@ -0,0 +1,7 @@
+import { JBrowsePluginMsaViewModel } from './model';
+export declare function doLaunchBlast({ self, }: {
+    self: JBrowsePluginMsaViewModel;
+}): Promise<{
+    msa: string;
+    tree: string;
+}>;

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -0,0 +1,27 @@
+import { launchMSA } from '../utils/msa';
+import { queryBlast } from '../utils/ncbiBlast';
+import { makeId, strip, } from '../LaunchMsaView/components/NewNCBIBlastQuery/util';
+export async function doLaunchBlast({ self, }) {
+    const { blastDatabase, blastProgram, msaAlgorithm, proteinSequence } = self.blastParams;
+    const query = proteinSequence.replaceAll('*', '').replaceAll('&', '');
+    const { hits } = await queryBlast({
+        query,
+        blastDatabase,
+        blastProgram,
+        onProgress: arg => self.setProgress(arg),
+        onRid: rid => self.setRid(rid),
+    });
+    const sequence = [
+        `>QUERY\n${query}`,
+        ...hits
+            .map(h => [makeId(h.description[0]), strip(h.hsps[0].hseq)])
+            .map(([id, seq]) => `>${id}\n${seq}`),
+    ].join('\n');
+    const data = await launchMSA({
+        algorithm: msaAlgorithm,
+        sequence,
+        onProgress: arg => self.setProgress(arg),
+    });
+    return data;
+}
+//# sourceMappingURL=doLaunchBlast.js.map

package/dist/MsaViewPanel/doLaunchBlast.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/genomeToMSA.d.ts

@@ -0,0 +1,4 @@
+import { JBrowsePluginMsaViewModel } from './model';
+export declare function genomeToMSA({ model }: {
+    model: JBrowsePluginMsaViewModel;
+}): number | undefined;

package/dist/MsaViewPanel/genomeToMSA.js

@@ -0,0 +1,18 @@
+import { getSession } from '@jbrowse/core/util';
+import { checkHovered } from './util';
+export function genomeToMSA({ model }) {
+    const { hovered } = getSession(model);
+    const { transcriptToMsaMap, connectedView } = model;
+    if (connectedView?.initialized &&
+        transcriptToMsaMap &&
+        checkHovered(hovered)) {
+        const { coord: hoverCoord } = hovered.hoverPosition;
+        const { g2p } = transcriptToMsaMap;
+        const ret = g2p[hoverCoord];
+        if (ret !== undefined) {
+            return model.seqCoordToRowSpecificGlobalCoord('QUERY', ret + 1);
+        }
+    }
+    return undefined;
+}
+//# sourceMappingURL=genomeToMSA.js.map

package/dist/MsaViewPanel/genomeToMSA.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/index.d.ts

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

package/dist/MsaViewPanel/index.js

@@ -0,0 +1,16 @@
+import { lazy } from 'react';
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
+// locals
+import stateModelFactory from './model';
+// lazies
+const MsaViewPanel = lazy(() => import('./components/MsaViewPanel'));
+export default function MsaViewF(pluginManager) {
+    pluginManager.addViewType(() => {
+        return new ViewType({
+            name: 'MsaView',
+            stateModel: stateModelFactory(),
+            ReactComponent: MsaViewPanel,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/MsaViewPanel/index.js.map

@@ -0,0 +1 @@
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