jbrowse-plugin-msaview 1.0.17 → 2.0.0

package/dist/MsaViewPanel/model.js

@@ -0,0 +1,235 @@
+import { addDisposer, cast, types } from 'mobx-state-tree';
+import { autorun } from 'mobx';
+import { MSAModelF } from 'react-msaview';
+import { getSession, notEmpty } from '@jbrowse/core/util';
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
+// locals
+import { doLaunchBlast } from './doLaunchBlast';
+import { genomeToMSA } from './genomeToMSA';
+import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
+/**
+ * #stateModel MsaViewPlugin
+ * extends
+ * - MSAModel from https://github.com/GMOD/react-msaview
+ */
+export default function stateModelFactory() {
+    return types
+        .compose(BaseViewModel, MSAModelF(), types.model('MsaView', {
+        /**
+         * #property
+         */
+        connectedViewId: types.maybe(types.string),
+        /**
+         * #property
+         */
+        connectedFeature: types.frozen(),
+        /**
+         * #property
+         */
+        connectedHighlights: types.array(types.model({
+            refName: types.string,
+            start: types.number,
+            end: types.number,
+        })),
+        /**
+         * #property
+         */
+        blastParams: types.frozen(),
+        /**
+         * #property
+         */
+        zoomToBaseLevel: false,
+    }))
+        .volatile(() => ({
+        rid: undefined,
+        progress: '',
+        error: undefined,
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
+        ungappedCoordMap(rowName, position) {
+            const row = self.rows.find(f => f[0] === rowName);
+            const seq = row?.[1];
+            if (seq && position < seq.length) {
+                let i = 0;
+                let j = 0;
+                for (; j < position; j++, i++) {
+                    while (seq[i] === '-') {
+                        i++;
+                    }
+                }
+                return i;
+            }
+            return undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get transcriptToMsaMap() {
+            console.log(self.connectedFeature);
+            return self.connectedFeature
+                ? genomeToTranscriptSeqMapping(self.connectedFeature)
+                : undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get mouseCol2() {
+            return genomeToMSA({ model: self });
+        },
+        /**
+         * #getter
+         */
+        get clickCol2() {
+            return undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get processing() {
+            return !!self.progress;
+        },
+        /**
+         * #getter
+         */
+        get connectedView() {
+            const { views } = getSession(self);
+            return views.find(f => f.id === self.connectedViewId);
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setZoomToBaseLevel(arg) {
+            self.zoomToBaseLevel = arg;
+        },
+        /**
+         * #action
+         */
+        setError(e) {
+            self.error = e;
+        },
+        /**
+         * #action
+         */
+        setProgress(arg) {
+            self.progress = arg;
+        },
+        /**
+         * #action
+         */
+        setRid(arg) {
+            self.rid = arg;
+        },
+        /**
+         * #action
+         */
+        setConnectedHighlights(r) {
+            self.connectedHighlights = cast(r);
+        },
+        /**
+         * #action
+         */
+        addToConnectedHighlights(r) {
+            self.connectedHighlights.push(r);
+        },
+        /**
+         * #action
+         */
+        clearConnectedHighlights() {
+            self.connectedHighlights = cast([]);
+        },
+        /**
+         * #action
+         */
+        setBlastParams(args) {
+            self.blastParams = args;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         * overrides base
+         */
+        extraViewMenuItems() {
+            return [
+                {
+                    label: 'Zoom to base level on click?',
+                    checked: self.zoomToBaseLevel,
+                    type: 'checkbox',
+                    onClick: () => self.setZoomToBaseLevel(!self.zoomToBaseLevel),
+                },
+            ];
+        },
+        /**
+         * #getter
+         */
+        get processing() {
+            return !!self.progress;
+        },
+        /**
+         * #getter
+         */
+        get connectedView() {
+            const { views } = getSession(self);
+            return views.find(f => f.id === self.connectedViewId);
+        },
+    }))
+        .actions(self => ({
+        afterCreate() {
+            addDisposer(self, autorun(async () => {
+                if (self.blastParams) {
+                    self.setProgress('Submitting query');
+                    const data = await doLaunchBlast({
+                        self: self,
+                    });
+                    self.setData(data);
+                    self.setBlastParams(undefined);
+                    self.setProgress('');
+                }
+            }));
+            // this adds highlights to the genome view when mouse-ing over the MSA
+            addDisposer(self, autorun(() => {
+                const { mouseCol, mouseClickCol } = self;
+                const r1 = mouseCol !== undefined
+                    ? msaCoordToGenomeCoord({ model: self, coord: mouseCol })
+                    : undefined;
+                const r2 = mouseClickCol !== undefined
+                    ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+                    : undefined;
+                self.setConnectedHighlights([r1, r2].filter(notEmpty));
+            }));
+            // nav to genome position after click
+            addDisposer(self, autorun(() => {
+                const { connectedView, zoomToBaseLevel, mouseClickCol } = self;
+                const { assemblyManager } = getSession(self);
+                const r2 = mouseClickCol !== undefined
+                    ? msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+                    : undefined;
+                if (!r2 || !connectedView) {
+                    return;
+                }
+                if (zoomToBaseLevel) {
+                    connectedView.navTo(r2);
+                }
+                else {
+                    const r = assemblyManager
+                        .get(connectedView.assemblyNames[0])
+                        ?.getCanonicalRefName(r2.refName) ?? r2.refName;
+                    connectedView.centerAt(r2.start, r);
+                }
+            }));
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map

package/dist/MsaViewPanel/model.js.map

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package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts

@@ -0,0 +1,9 @@
+import { JBrowsePluginMsaViewModel } from './model';
+export declare function msaCoordToGenomeCoord({ model, coord: mouseCol, }: {
+    model: JBrowsePluginMsaViewModel;
+    coord: number;
+}): {
+    refName: string;
+    start: number;
+    end: number;
+} | undefined;

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -0,0 +1,20 @@
+export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
+    const { transcriptToMsaMap } = model;
+    if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+        return;
+    }
+    const c = mouseCol - 1;
+    const k1 = model.globalCoordToRowSpecificSeqCoord('QUERY', c) || 0;
+    const k2 = model.globalCoordToRowSpecificSeqCoord('QUERY', c + 1) || 0;
+    const { refName, p2g } = transcriptToMsaMap;
+    const s = p2g[k1];
+    const e = p2g[k2];
+    return s !== undefined && e !== undefined
+        ? {
+            refName,
+            start: Math.min(s, e),
+            end: Math.max(s, e),
+        }
+        : undefined;
+}
+//# sourceMappingURL=msaCoordToGenomeCoord.js.map

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map

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

@@ -0,0 +1,8 @@
+import { Feature } from '@jbrowse/core/util';
+export declare function checkHovered(hovered: unknown): hovered is {
+    hoverFeature: Feature;
+    hoverPosition: {
+        coord: number;
+        refName: string;
+    };
+};

package/dist/MsaViewPanel/util.js

@@ -0,0 +1,7 @@
+export function checkHovered(hovered) {
+    return (!!hovered &&
+        typeof hovered == 'object' &&
+        'hoverFeature' in hovered &&
+        'hoverPosition' in hovered);
+}
+//# sourceMappingURL=util.js.map

package/dist/MsaViewPanel/util.js.map

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

@@ -0,0 +1,3 @@
+import React from 'react';
+import { SvgIconProps } from '@mui/material';
+export default function OpenInNewIcon(props: SvgIconProps): React.JSX.Element;

package/dist/OpenInNewIcon.js

@@ -0,0 +1,8 @@
+import React from 'react';
+import { SvgIcon } from '@mui/material';
+export default function OpenInNewIcon(props) {
+    return (React.createElement(SvgIcon, { ...props },
+        React.createElement("path", { d: "M0 0h24v24H0z", fill: "none" }),
+        React.createElement("path", { d: "M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z" })));
+}
+//# sourceMappingURL=OpenInNewIcon.js.map

package/dist/OpenInNewIcon.js.map

@@ -0,0 +1 @@
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package/dist/TextField2.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+import { TextFieldProps } from '@mui/material';
+declare function TextField2({ children, ...rest }: TextFieldProps): React.JSX.Element;
+export default TextField2;

package/dist/TextField2.js

@@ -0,0 +1,8 @@
+import React from 'react';
+import { TextField } from '@mui/material';
+function TextField2({ children, ...rest }) {
+    return (React.createElement("div", null,
+        React.createElement(TextField, { ...rest }, children)));
+}
+export default TextField2;
+//# sourceMappingURL=TextField2.js.map

package/dist/TextField2.js.map

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

@@ -1,8 +1,8 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-export default class MsaViewPlugin extends Plugin {
-    name: string;
-    version: any;
-    install(pluginManager: PluginManager): void;
-    configure(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class MsaViewPlugin extends Plugin {
+    name: string;
+    version: any;
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -1,8 +1,33 @@
-
-'use strict'
-
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./jbrowse-plugin-msaview.cjs.production.min.js')
-} else {
-  module.exports = require('./jbrowse-plugin-msaview.cjs.development.js')
+import Plugin from '@jbrowse/core/Plugin';
+import { isAbstractMenuManager } from '@jbrowse/core/util';
+// icons
+import GridOn from '@mui/icons-material/GridOn';
+// locals
+import { version } from '../package.json';
+import MsaViewF from './MsaViewPanel';
+import LaunchMsaViewF from './LaunchMsaView';
+import AddHighlightModelF from './AddHighlightModel';
+export default class MsaViewPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'MsaViewPlugin';
+        this.version = version;
+    }
+    install(pluginManager) {
+        MsaViewF(pluginManager);
+        LaunchMsaViewF(pluginManager);
+        AddHighlightModelF(pluginManager);
+    }
+    configure(pluginManager) {
+        if (isAbstractMenuManager(pluginManager.rootModel)) {
+            pluginManager.rootModel.appendToSubMenu(['Add'], {
+                label: 'Multiple sequence alignment view',
+                icon: GridOn,
+                onClick: (session) => {
+                    session.addView('MsaView', {});
+                },
+            });
+        }
+    }
 }
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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