@jbrowse/plugin-sv-inspector 2.6.1

package/esm/SvInspectorView/models/SvInspectorView.js

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+import clone from 'clone';
+import { autorun, reaction } from 'mobx';
+import { types, getParent, addDisposer } from 'mobx-state-tree';
+import { getSession } from '@jbrowse/core/util';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
+// icons
+import OpenInNewIcon from '@mui/icons-material/OpenInNew';
+import FolderOpenIcon from '@mui/icons-material/FolderOpen';
+// locals
+import { canOpenBreakpointSplitViewFromTableRow, openBreakpointSplitViewFromTableRow, getFeatureForRow, } from './breakpointSplitViewFromTableRow';
+/**
+ * #stateModel SvInspectorView
+ * #category view
+ * combination of a spreadsheetview and a circularview
+ */
+function SvInspectorViewF(pluginManager) {
+    const SpreadsheetViewType = pluginManager.getViewType('SpreadsheetView');
+    const CircularViewType = pluginManager.getViewType('CircularView');
+    const SpreadsheetModel = SpreadsheetViewType.stateModel;
+    const CircularModel = CircularViewType.stateModel;
+    const minHeight = 400;
+    const defaultHeight = 550;
+    const headerHeight = 52;
+    const circularViewOptionsBarHeight = 52;
+    return types
+        .compose(BaseViewModel, types.model('SvInspectorView', {
+        /**
+         * #property
+         */
+        id: ElementId,
+        /**
+         * #property
+         */
+        type: types.literal('SvInspectorView'),
+        /**
+         * #property
+         */
+        height: types.optional(types.refinement('SvInspectorViewHeight', types.number, n => n >= minHeight), defaultHeight),
+        /**
+         * #property
+         */
+        onlyDisplayRelevantRegionsInCircularView: false,
+        /**
+         * #property
+         * switch specifying whether we are showing the import wizard or the
+         * spreadsheet in our viewing area
+         */
+        mode: types.optional(types.enumeration('SvInspectorViewMode', ['import', 'display']), 'import'),
+        /**
+         * #property
+         */
+        spreadsheetView: types.optional(SpreadsheetModel, () => SpreadsheetModel.create({
+            type: 'SpreadsheetView',
+            hideVerticalResizeHandle: true,
+        })),
+        /**
+         * #property
+         */
+        circularView: types.optional(CircularModel, () => CircularModel.create({
+            type: 'CircularView',
+            hideVerticalResizeHandle: true,
+            hideTrackSelectorButton: true,
+            disableImportForm: true,
+        })),
+    }))
+        .volatile(() => ({
+        width: 800,
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get selectedRows() {
+            // @ts-expect-error
+            return self.spreadsheetView.rowSet.selectedRows;
+        },
+        /**
+         * #getter
+         */
+        get assemblyName() {
+            const { assembly } = self.spreadsheetView;
+            return assembly ? readConfObject(assembly, 'name') : undefined;
+        },
+        /**
+         * #getter
+         */
+        get showCircularView() {
+            return self.spreadsheetView.mode === 'display';
+        },
+        /**
+         * #getter
+         */
+        get features() {
+            const session = getSession(self);
+            const { spreadsheetView } = self;
+            const { outputRows = [] } = spreadsheetView;
+            return outputRows
+                .map((r, i) => getFeatureForRow(session, spreadsheetView, r, i))
+                .filter(f => !!f);
+        },
+        /**
+         * #getter
+         */
+        get featuresAdapterConfigSnapshot() {
+            return {
+                type: 'FromConfigAdapter',
+                features: this.features,
+            };
+        },
+        /**
+         * #getter
+         */
+        get featureRefNames() {
+            const refs = this.features.map(r => r.refName);
+            const CHR2 = this.features.flatMap(r => { var _a; return (_a = r.INFO) === null || _a === void 0 ? void 0 : _a.CHR2; }).filter(f => !!f);
+            return [...refs, ...CHR2];
+        },
+        /**
+         * #getter
+         */
+        get featuresCircularTrackConfiguration() {
+            return {
+                type: 'VariantTrack',
+                trackId: `sv-inspector-variant-track-${self.id}`,
+                name: 'features from tabular data',
+                adapter: this.featuresAdapterConfigSnapshot,
+                assemblyNames: [this.assemblyName],
+                displays: [
+                    {
+                        type: 'ChordVariantDisplay',
+                        displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
+                        onChordClick: `jexl:defaultOnChordClick(feature, track, pluginManager)`,
+                        renderer: { type: 'StructuralVariantChordRenderer' },
+                    },
+                ],
+            };
+        },
+    }))
+        .volatile(() => ({
+        SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent,
+        CircularViewReactComponent: CircularViewType.ReactComponent,
+        circularViewOptionsBarHeight,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setWidth(newWidth) {
+            self.width = newWidth;
+        },
+        /**
+         * #action
+         */
+        setHeight(newHeight) {
+            self.height = newHeight > minHeight ? newHeight : minHeight;
+            return self.height;
+        },
+        /**
+         * #action
+         */
+        setImportMode() {
+            self.spreadsheetView.setImportMode();
+        },
+        /**
+         * #action
+         */
+        setDisplayMode() {
+            self.spreadsheetView.setDisplayMode();
+        },
+        /**
+         * #action
+         */
+        closeView() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            getParent(self, 2).removeView(self);
+        },
+        /**
+         * #action
+         */
+        setDisplayedRegions(regions) {
+            self.circularView.setDisplayedRegions(regions);
+        },
+        /**
+         * #action
+         */
+        setOnlyDisplayRelevantRegionsInCircularView(val) {
+            self.onlyDisplayRelevantRegionsInCircularView = Boolean(val);
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
+        menuItems() {
+            return [
+                {
+                    label: 'Return to import form',
+                    onClick: () => self.setImportMode(),
+                    icon: FolderOpenIcon,
+                },
+            ];
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        resizeHeight(distance) {
+            const oldHeight = self.height;
+            const newHeight = self.setHeight(self.height + distance);
+            return newHeight - oldHeight;
+        },
+        afterAttach() {
+            // synchronize subview widths
+            addDisposer(self, autorun(() => {
+                const borderWidth = 1;
+                if (self.showCircularView) {
+                    const spreadsheetWidth = Math.round(self.width * 0.66);
+                    const circularViewWidth = self.width - spreadsheetWidth;
+                    self.spreadsheetView.setWidth(spreadsheetWidth - borderWidth);
+                    self.circularView.setWidth(circularViewWidth);
+                }
+                else {
+                    self.spreadsheetView.setWidth(self.width);
+                }
+            }, { name: 'SvInspectorView width binding' }));
+            // synchronize subview heights
+            addDisposer(self, autorun(() => {
+                self.spreadsheetView.setHeight(self.height - headerHeight);
+                self.circularView.setHeight(self.height - headerHeight - circularViewOptionsBarHeight);
+            }, { name: 'SvInspectorView height binding' }));
+            // bind circularview displayedRegions to spreadsheet assembly, mediated
+            // by the onlyRelevantRegions toggle
+            addDisposer(self, autorun(async () => {
+                const { assemblyName, onlyDisplayRelevantRegionsInCircularView, circularView, featureRefNames, } = self;
+                const { tracks } = circularView;
+                const { assemblyManager } = getSession(self);
+                if (!assemblyName) {
+                    return;
+                }
+                const asm = await assemblyManager.waitForAssembly(assemblyName);
+                if (!asm) {
+                    return;
+                }
+                const { getCanonicalRefName, regions = [] } = asm;
+                if (onlyDisplayRelevantRegionsInCircularView) {
+                    if (tracks.length === 1) {
+                        try {
+                            // canonicalize the store's ref names if necessary
+                            const refSet = new Set(featureRefNames.map(r => getCanonicalRefName(r) || r));
+                            circularView.setDisplayedRegions(clone(regions.filter(r => refSet.has(r.refName))));
+                        }
+                        catch (e) {
+                            circularView.setError(e);
+                        }
+                    }
+                }
+                else {
+                    circularView.setDisplayedRegions(regions);
+                }
+            }, { name: 'SvInspectorView displayed regions bind' }));
+            // bind circularview tracks to our track snapshot view
+            addDisposer(self, reaction(() => ({
+                generatedTrackConf: self === null || self === void 0 ? void 0 : self.featuresCircularTrackConfiguration,
+                assemblyName: self === null || self === void 0 ? void 0 : self.assemblyName,
+            }), data => {
+                if (!data) {
+                    return;
+                }
+                const { assemblyName, generatedTrackConf } = data;
+                const { circularView } = self;
+                // hide any visible tracks
+                circularView.tracks.forEach(t => circularView.hideTrack(t.configuration.trackId));
+                // put our track in as the only track
+                if (assemblyName && generatedTrackConf) {
+                    // @ts-expect-error
+                    circularView.addTrackConf(generatedTrackConf, {
+                        assemblyName,
+                    });
+                }
+            }, {
+                name: 'SvInspectorView track configuration binding',
+                fireImmediately: true,
+            }));
+            // bind spreadsheetView row menu actions to us
+            addDisposer(self, autorun(() => {
+                self.spreadsheetView.setRowMenuItems(
+                // these are the MenuItem entries for the row menu actions in the
+                // spreadsheet view.  these are installed into the child
+                // SpreadsheetView using an autorun below
+                [
+                    {
+                        label: 'Open split detail view',
+                        icon: OpenInNewIcon,
+                        // @ts-expect-error
+                        disabled(spreadsheetView, spreadsheet, rowNumber, row) {
+                            return !canOpenBreakpointSplitViewFromTableRow(self, spreadsheetView, spreadsheet, row, rowNumber);
+                        },
+                        // @ts-expect-error
+                        onClick(spreadsheetView, spreadsheet, rowNumber, row) {
+                            openBreakpointSplitViewFromTableRow(self, spreadsheetView, spreadsheet, row, rowNumber);
+                        },
+                    },
+                ]);
+            }));
+        },
+    }));
+}
+export default SvInspectorViewF;
+//# sourceMappingURL=SvInspectorView.js.map

package/esm/SvInspectorView/models/SvInspectorView.js.map

@@ -0,0 +1 @@
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package/esm/SvInspectorView/models/adhocFeatureUtils.d.ts

@@ -0,0 +1,44 @@
+export function makeAdHocFeature(columns: any, columnsAlreadyUsedInLocations: any, row: any, loc1: any, loc2: any, rowNumber: any): {
+    uniqueId: string;
+    refName: any;
+    start: any;
+    end: any;
+    mate: {
+        refName: any;
+        start: any;
+        end: any;
+    };
+};
+export function makeAdHocSvFeatureFromTwoLocations(columns: any, locationColumnNumbers: any, row: any, rowNumber: any, isValidRefName: any): {
+    uniqueId: string;
+    refName: any;
+    start: any;
+    end: any;
+    mate: {
+        refName: any;
+        start: any;
+        end: any;
+    };
+};
+export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns: any, locRefColumnNumbers: any, locStartColumnNumbers: any, locEndColumnNumbers: any, row: any, rowNumber: any): {
+    uniqueId: string;
+    refName: any;
+    start: any;
+    end: any;
+    mate: {
+        refName: any;
+        start: any;
+        end: any;
+    };
+};
+export function makeAdHocSvFeature(sheet: any, rowNumber: any, row: any, isValidRefName: any): {
+    uniqueId: string;
+    refName: any;
+    start: any;
+    end: any;
+    mate: {
+        refName: any;
+        start: any;
+        end: any;
+    };
+} | undefined;

package/esm/SvInspectorView/models/adhocFeatureUtils.js

@@ -0,0 +1,90 @@
+// this file contains the rather verbose functions for
+// creating features from CSV/TSV lines
+import { parseLocString } from '@jbrowse/core/util';
+export function makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber) {
+    // load all the other data in the row into an `otherData` object
+    const otherData = {};
+    columns.forEach((column, columnNumber) => {
+        if (columnsAlreadyUsedInLocations.includes(columnNumber)) {
+            return;
+        }
+        let { text } = row.cells[columnNumber];
+        if (column.dataType.type === 'Number') {
+            text = parseFloat(text);
+        }
+        otherData[column.name] = text;
+    });
+    // make the final feature data out of otherData + the parsed locations
+    return {
+        ...otherData,
+        uniqueId: `sv-inspector-adhoc-${rowNumber}`,
+        refName: loc1.refName,
+        start: loc1.start,
+        end: loc1.end,
+        mate: {
+            refName: loc2.refName,
+            start: loc2.start,
+            end: loc2.end,
+        },
+    };
+}
+export function makeAdHocSvFeatureFromTwoLocations(columns, locationColumnNumbers, row, rowNumber, isValidRefName) {
+    // use the first two locations we found (first according to *displayed* order)
+    const loc1 = parseLocString(row.cells[locationColumnNumbers[0]].text, isValidRefName);
+    const loc2 = parseLocString(row.cells[locationColumnNumbers[1]].text, isValidRefName);
+    const columnsAlreadyUsedInLocations = [
+        locationColumnNumbers[0],
+        locationColumnNumbers[1],
+    ];
+    return makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber);
+}
+export function makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNumbers, locStartColumnNumbers, locEndColumnNumbers, row, rowNumber) {
+    const textOf = colno => row.cells[colno].text;
+    const loc1 = {
+        refName: textOf(locRefColumnNumbers[0]),
+        start: parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
+        end: parseInt(textOf(locEndColumnNumbers[0]), 10),
+    };
+    const loc2 = {
+        refName: textOf(locRefColumnNumbers[1]),
+        start: parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
+        end: parseInt(textOf(locEndColumnNumbers[1]), 10),
+    };
+    const columnsAlreadyUsedInLocations = [
+        locRefColumnNumbers[0],
+        locStartColumnNumbers[0],
+        locEndColumnNumbers[0],
+        locRefColumnNumbers[1],
+        locStartColumnNumbers[1],
+        locEndColumnNumbers[1],
+    ];
+    return makeAdHocFeature(columns, columnsAlreadyUsedInLocations, row, loc1, loc2, rowNumber);
+}
+// makes a feature data object (passed as `data` to a SimpleFeature constructor)
+// out of table row if the row has 2 location columns. undefined if not
+export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
+    const { columns, columnDisplayOrder } = sheet;
+    const columnTypes = {};
+    columnDisplayOrder.forEach(columnNumber => {
+        const columnDefinition = columns[columnNumber];
+        if (!columnTypes[columnDefinition.dataType.type]) {
+            columnTypes[columnDefinition.dataType.type] = [];
+        }
+        columnTypes[columnDefinition.dataType.type].push(columnNumber);
+    });
+    const locationColumnNumbers = columnTypes.LocString || [];
+    const locStartColumnNumbers = columnTypes.LocStart || [];
+    const locEndColumnNumbers = columnTypes.LocEnd || [];
+    const locRefColumnNumbers = columnTypes.LocRef || [];
+    // if we have 2 or more columns of type location, make a feature from them
+    if (locationColumnNumbers.length >= 2) {
+        return makeAdHocSvFeatureFromTwoLocations(columns, locationColumnNumbers, row, rowNumber, isValidRefName);
+    }
+    if (locRefColumnNumbers.length >= 2 &&
+        locStartColumnNumbers.length >= 2 &&
+        locEndColumnNumbers.length >= 2) {
+        return makeAdHocSvFeatureFromTwoRefStartEndSets(columns, locRefColumnNumbers, locStartColumnNumbers, locEndColumnNumbers, row, rowNumber);
+    }
+    return undefined;
+}
+//# sourceMappingURL=adhocFeatureUtils.js.map

package/esm/SvInspectorView/models/adhocFeatureUtils.js.map

@@ -0,0 +1 @@
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package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.d.ts

@@ -0,0 +1,4 @@
+export function getFeatureForRow(session: any, spreadsheetView: any, row: any, rowNumber: any): any;
+export function breakpointSplitViewSnapshotFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): any;
+export function openBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): void;
+export function canOpenBreakpointSplitViewFromTableRow(svInspectorView: any, spreadsheetView: any, spreadsheet: any, row: any, rowNumber: any): boolean;

package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -0,0 +1,42 @@
+import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util';
+import { makeAdHocSvFeature } from './adhocFeatureUtils';
+export function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
+    var _a, _b;
+    return (((_a = row.extendedData) === null || _a === void 0 ? void 0 : _a.vcfFeature) ||
+        ((_b = row.extendedData) === null || _b === void 0 ? void 0 : _b.feature) ||
+        makeAdHocSvFeature(spreadsheetView.spreadsheet, rowNumber, row, session.assemblyManager.isValidRefName));
+}
+export function breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
+    const { pluginManager } = getEnv(svInspectorView);
+    const session = getSession(spreadsheetView);
+    const featureData = getFeatureForRow(session, spreadsheet, row, rowNumber);
+    if (featureData) {
+        const feature = new SimpleFeature(featureData);
+        session.setSelection(feature);
+        return pluginManager
+            .getViewType('BreakpointSplitView')
+            .snapshotFromBreakendFeature(feature, svInspectorView.circularView);
+    }
+    return undefined;
+}
+export function openBreakpointSplitViewFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
+    const viewSnapshot = breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber);
+    if (viewSnapshot) {
+        // try to center the offsetPx
+        const { circularView } = svInspectorView;
+        viewSnapshot.views[0].offsetPx -= circularView.width / 2 + 100;
+        viewSnapshot.views[1].offsetPx -= circularView.width / 2 + 100;
+        const session = getSession(spreadsheetView);
+        session.addView('BreakpointSplitView', viewSnapshot);
+    }
+}
+export function canOpenBreakpointSplitViewFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber) {
+    try {
+        return Boolean(breakpointSplitViewSnapshotFromTableRow(svInspectorView, spreadsheetView, spreadsheet, row, rowNumber));
+    }
+    catch (e) {
+        console.error('Unable to open breakpoint split view from table row', e);
+        return false;
+    }
+}
+//# sourceMappingURL=breakpointSplitViewFromTableRow.js.map

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package/esm/index.d.ts

@@ -0,0 +1,7 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import Plugin from '@jbrowse/core/Plugin';
+export default class SvInspectorViewPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,29 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { isAbstractMenuManager, } from '@jbrowse/core/util/types';
+// icons
+import TableChartIcon from '@mui/icons-material/TableChart';
+// locals
+import SvInspectorViewF from './SvInspectorView';
+import LaunchSvInspectorViewF from './LaunchSvInspectorView';
+export default class SvInspectorViewPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'SvInspectorViewPlugin';
+    }
+    install(pluginManager) {
+        SvInspectorViewF(pluginManager);
+        LaunchSvInspectorViewF(pluginManager);
+    }
+    configure(pluginManager) {
+        if (isAbstractMenuManager(pluginManager.rootModel)) {
+            pluginManager.rootModel.appendToSubMenu(['Add'], {
+                label: 'SV inspector',
+                icon: TableChartIcon,
+                onClick: (session) => {
+                    session.addView('SvInspectorView', {});
+                },
+            });
+        }
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/package.json

@@ -0,0 +1,62 @@
+{
+  "name": "@jbrowse/plugin-sv-inspector",
+  "version": "2.6.1",
+  "description": "JBrowse 2 SV inspector view",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/sv-inspector"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "dist/index.js",
+  "files": [
+    "dist",
+    "src",
+    "esm"
+  ],
+  "scripts": {
+    "build": "npm-run-all build:*",
+    "test": "cd ../..; jest plugins/sv-inspector",
+    "prepublishOnly": "yarn test",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
+  },
+  "dependencies": {
+    "@mui/icons-material": "^5.0.1",
+    "clone": "^2.1.2"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-circular-view": "^2.0.0",
+    "@jbrowse/plugin-spreadsheet-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "react": ">=16.8.0",
+    "react-dom": ">=16.8.0",
+    "tss-react": "^4.0.0"
+  },
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}