@jbrowse/plugin-sv-inspector 2.17.0 → 2.18.0

package/dist/SvInspectorView/{models/SvInspectorView.js → model.js}

@@ -3,28 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const clone_1 = __importDefault(require("clone"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
-const mst_1 = require("@jbrowse/core/util/types/mst");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-// icons
-const OpenInNew_1 = __importDefault(require("@mui/icons-material/OpenInNew"));
+const util_1 = require("@jbrowse/core/util");
+const mst_1 = require("@jbrowse/core/util/types/mst");
 const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
-// locals
-const breakpointSplitViewFromTableRow_1 = require("./breakpointSplitViewFromTableRow");
-/**
- * #stateModel SvInspectorView
- * #category view
- * does not extend, but is a combination of a
- * - [SpreadsheetView](../spreadsheetview)
- * - [CircularView](../circularview)
- *
- * extends
- * - [BaseViewModel](../baseviewmodel)
- */
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function SvInspectorViewF(pluginManager) {
     const SpreadsheetViewType = pluginManager.getViewType('SpreadsheetView');
     const CircularViewType = pluginManager.getViewType('CircularView');
@@ -36,38 +21,14 @@ function SvInspectorViewF(pluginManager) {
     const circularViewOptionsBarHeight = 52;
     return mobx_state_tree_1.types
         .compose('SvInspectorView', models_1.BaseViewModel, mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('SvInspectorView'),
-        /**
-         * #property
-         */
-        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.refinement('SvInspectorViewHeight', mobx_state_tree_1.types.number, n => n >= minHeight), defaultHeight),
-        /**
-         * #property
-         */
+        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, defaultHeight),
         onlyDisplayRelevantRegionsInCircularView: false,
-        /**
-         * #property
-         * switch specifying whether we are showing the import wizard or the
-         * spreadsheet in our viewing area
-         */
-        mode: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.enumeration('SvInspectorViewMode', ['import', 'display']), 'import'),
-        /**
-         * #property
-         */
         spreadsheetView: mobx_state_tree_1.types.optional(SpreadsheetModel, () => SpreadsheetModel.create({
             type: 'SpreadsheetView',
             hideVerticalResizeHandle: true,
         })),
-        /**
-         * #property
-         */
         circularView: mobx_state_tree_1.types.optional(CircularModel, () => CircularModel.create({
             type: 'CircularView',
             hideVerticalResizeHandle: true,
@@ -77,61 +38,51 @@ function SvInspectorViewF(pluginManager) {
     }))
         .volatile(() => ({
         width: 800,
+        SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent,
+        CircularViewReactComponent: CircularViewType.ReactComponent,
+        circularViewOptionsBarHeight,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
-        get selectedRows() {
-            var _a;
-            return (_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet.selectedRows;
-        },
-        /**
-         * #getter
-         */
         get assemblyName() {
             const { assembly } = self.spreadsheetView;
             return assembly
                 ? (0, configuration_1.readConfObject)(assembly, 'name')
                 : undefined;
         },
-        /**
-         * #getter
-         */
         get showCircularView() {
-            return self.spreadsheetView.mode === 'display';
+            return !!self.spreadsheetView.spreadsheet;
         },
-        /**
-         * #getter
-         */
         get features() {
-            const session = (0, util_1.getSession)(self);
-            const { spreadsheetView } = self;
-            const { outputRows = [] } = spreadsheetView;
-            return outputRows
-                .map((r, i) => (0, breakpointSplitViewFromTableRow_1.getFeatureForRow)(session, spreadsheetView, r, i))
-                .filter(f => !!f);
+            var _a, _b;
+            return (((_b = structuredClone((_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.visibleRows)) === null || _b === void 0 ? void 0 : _b.map(row => row.feature).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];
+            return [
+                ...new Set([
+                    ...this.features.map(r => r.refName),
+                    ...this.features.flatMap(r => { var _a; return (_a = r.INFO) === null || _a === void 0 ? void 0 : _a.CHR2; }),
+                    ...this.features.flatMap(r => { var _a; return (_a = r.mate) === null || _a === void 0 ? void 0 : _a.refName; }),
+                ].filter(f => !!f)),
+            ];
+        },
+        get currentAssembly() {
+            const { assemblyManager } = (0, util_1.getSession)(self);
+            return this.assemblyName
+                ? assemblyManager.get(this.assemblyName)
+                : undefined;
+        },
+        get canonicalFeatureRefNameSet() {
+            const asm = this.currentAssembly;
+            return new Set((asm === null || asm === void 0 ? void 0 : asm.initialized)
+                ? this.featureRefNames.map(r => asm.getCanonicalRefName(r) || r)
+                : []);
         },
-        /**
-         * #getter
-         */
         get featuresCircularTrackConfiguration() {
             return {
                 type: 'VariantTrack',
@@ -144,83 +95,49 @@ function SvInspectorViewF(pluginManager) {
                         type: 'ChordVariantDisplay',
                         displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
                         onChordClick: 'jexl:defaultOnChordClick(feature, track, pluginManager)',
-                        renderer: { type: 'StructuralVariantChordRenderer' },
+                        renderer: {
+                            type: 'StructuralVariantChordRenderer',
+                        },
                     },
                 ],
             };
         },
-    }))
-        .volatile(() => ({
-        SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent,
-        CircularViewReactComponent: CircularViewType.ReactComponent,
-        circularViewOptionsBarHeight,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setWidth(newWidth) {
             self.width = newWidth;
         },
-        /**
-         * #action
-         */
         setHeight(newHeight) {
             self.height = Math.max(newHeight, minHeight);
             return self.height;
         },
-        /**
-         * #action
-         */
-        setImportMode() {
-            self.spreadsheetView.setImportMode();
-        },
-        /**
-         * #action
-         */
-        setDisplayMode() {
-            self.spreadsheetView.setDisplayMode();
-        },
-        /**
-         * #action
-         */
         setDisplayedRegions(regions) {
             self.circularView.setDisplayedRegions(regions);
         },
-        /**
-         * #action
-         */
         setOnlyDisplayRelevantRegionsInCircularView(val) {
             self.onlyDisplayRelevantRegionsInCircularView = Boolean(val);
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         menuItems() {
             return [
                 {
                     label: 'Return to import form',
+                    icon: FolderOpen_1.default,
                     onClick: () => {
-                        self.setImportMode();
+                        self.spreadsheetView.displaySpreadsheet(undefined);
                     },
-                    icon: FolderOpen_1.default,
                 },
             ];
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = self.setHeight(self.height + distance);
             return newHeight - oldHeight;
         },
         afterAttach() {
-            // synchronize subview widths
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 const borderWidth = 1;
                 if (self.showCircularView) {
@@ -233,53 +150,41 @@ function SvInspectorViewF(pluginManager) {
                     self.spreadsheetView.setWidth(self.width);
                 }
             }, { name: 'SvInspectorView width binding' }));
-            // synchronize subview heights
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.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
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                const { assemblyName, onlyDisplayRelevantRegionsInCircularView, circularView, featureRefNames, } = self;
-                const { tracks } = circularView;
-                const { assemblyManager } = (0, util_1.getSession)(self);
-                if (!assemblyName) {
-                    return;
-                }
-                const asm = await assemblyManager.waitForAssembly(assemblyName);
-                if (!asm) {
+                const { onlyDisplayRelevantRegionsInCircularView, circularView, canonicalFeatureRefNameSet, currentAssembly, } = self;
+                if (!circularView.initialized || !(currentAssembly === null || currentAssembly === void 0 ? void 0 : currentAssembly.regions)) {
                     return;
                 }
-                const { getCanonicalRefName, regions = [] } = asm;
                 if (onlyDisplayRelevantRegionsInCircularView) {
-                    if (tracks.length === 1) {
+                    if (circularView.tracks.length === 1) {
                         try {
-                            // canonicalize the store's ref names if necessary
-                            const refSet = new Set(featureRefNames.map(r => getCanonicalRefName(r) || r));
-                            circularView.setDisplayedRegions((0, clone_1.default)(regions.filter(r => refSet.has(r.refName))));
+                            circularView.setDisplayedRegions(structuredClone(currentAssembly.regions.filter(r => canonicalFeatureRefNameSet.has(r.refName))));
                         }
                         catch (e) {
-                            circularView.setError(e);
+                            console.error(e);
+                            (0, util_1.getSession)(self).notifyError(`${e}`, e);
                         }
                     }
                 }
                 else {
-                    circularView.setDisplayedRegions(regions);
+                    circularView.setDisplayedRegions(currentAssembly.regions);
                 }
             }, { name: 'SvInspectorView displayed regions bind' }));
-            // bind circularview tracks to our track snapshot view
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => ({
                 generatedTrackConf: self.featuresCircularTrackConfiguration,
                 assemblyName: 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) {
-                    // @ts-expect-error
                     circularView.addTrackConf(generatedTrackConf, {
                         assemblyName,
                     });
@@ -288,27 +193,11 @@ function SvInspectorViewF(pluginManager) {
                 name: 'SvInspectorView track configuration binding',
                 fireImmediately: true,
             }));
-            // bind spreadsheetView row menu actions to us
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.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: OpenInNew_1.default,
-                        // @ts-expect-error
-                        disabled(spreadsheetView, spreadsheet, rowNumber, row) {
-                            return !(0, breakpointSplitViewFromTableRow_1.canOpenBreakpointSplitViewFromTableRow)(self, spreadsheetView, spreadsheet, row, rowNumber);
-                        },
-                        onClick(spreadsheetView, spreadsheet, rowNumber, row) {
-                            (0, breakpointSplitViewFromTableRow_1.openBreakpointSplitViewFromTableRow)(self, spreadsheetView, spreadsheet, row, rowNumber);
-                        },
-                    },
-                ]);
-            }));
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        const { circularView, ...rest } = snap;
+        return rest;
+    });
 }
 exports.default = SvInspectorViewF;

package/dist/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class SvInspectorViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -5,11 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const types_1 = require("@jbrowse/core/util/types");
-// icons
 const TableChart_1 = __importDefault(require("@mui/icons-material/TableChart"));
-// locals
-const SvInspectorView_1 = __importDefault(require("./SvInspectorView"));
 const LaunchSvInspectorView_1 = __importDefault(require("./LaunchSvInspectorView"));
+const SvInspectorView_1 = __importDefault(require("./SvInspectorView"));
 class SvInspectorViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/esm/LaunchSvInspectorView/index.d.ts

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

package/esm/LaunchSvInspectorView/index.js

@@ -1,7 +1,5 @@
 export default function LaunchSvInspectorViewF(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-SvInspectorView', 
-    // @ts-expect-error
-    async ({ session, assembly, uri, fileType, }) => {
+    pluginManager.addToExtensionPoint('LaunchView-SvInspectorView', async ({ session, assembly, uri, fileType, }) => {
         var _a, _b;
         const view = session.addView('SvInspectorView');
         const exts = uri.split('.');

package/esm/SvInspectorView/components/CircularViewOptions.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SvInspectorViewModel } from '../models/SvInspectorView';
+import type { SvInspectorViewModel } from '../model';
 declare const CircularViewOptions: ({ svInspector, }: {
     svInspector: SvInspectorViewModel;
 }) => React.JSX.Element;

package/esm/SvInspectorView/components/CircularViewOptions.js

@@ -1,6 +1,6 @@
 import React from 'react';
+import { Checkbox, FormControlLabel, Grid } from '@mui/material';
 import { observer } from 'mobx-react';
-import { Grid, FormControlLabel, Checkbox } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     circularViewOptions: {

package/esm/SvInspectorView/components/SvInspectorView.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SvInspectorViewModel } from '../models/SvInspectorView';
+import type { SvInspectorViewModel } from '../model';
 declare const SvInspectorView: ({ model, }: {
     model: SvInspectorViewModel;
 }) => React.JSX.Element;

package/esm/SvInspectorView/components/SvInspectorView.js

@@ -1,7 +1,7 @@
 import React from 'react';
+import { ResizeHandle } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { ResizeHandle } from '@jbrowse/core/ui';
 import CircularViewOptions from './CircularViewOptions';
 const useStyles = makeStyles()(theme => ({
     resizeHandleVert: {

package/esm/SvInspectorView/index.d.ts

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

package/esm/SvInspectorView/index.js

@@ -1,17 +1,30 @@
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import ReactComponent from './components/SvInspectorView';
-import stateModelFactory from './models/SvInspectorView';
 import { getContainingView, getSession } from '@jbrowse/core/util';
-function defaultOnChordClick(feature, chordTrack, pluginManager) {
-    const session = getSession(chordTrack);
-    session.setSelection(feature);
-    const view = getContainingView(chordTrack);
-    const viewType = pluginManager.getViewType('BreakpointSplitView');
-    const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
-    // try to center the offsetPx
-    viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
-    viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
-    session.addView('BreakpointSplitView', viewSnapshot);
+import { navToMultiLevelBreak } from '@jbrowse/sv-core';
+import { getParent } from 'mobx-state-tree';
+import ReactComponent from './components/SvInspectorView';
+import stateModelFactory from './model';
+function defaultOnChordClick(feature, chordTrack) {
+    ;
+    (async () => {
+        const session = getSession(chordTrack);
+        try {
+            session.setSelection(feature);
+            const view = getContainingView(chordTrack);
+            const parentView = getParent(view);
+            const stableViewId = `${parentView.id}_spawned`;
+            await navToMultiLevelBreak({
+                assemblyName: view.assemblyNames[0],
+                session,
+                stableViewId,
+                feature,
+            });
+        }
+        catch (e) {
+            console.error(e);
+            session.notifyError(`${e}`, e);
+        }
+    })();
 }
 export default function SvInspectorViewF(pluginManager) {
     pluginManager.jexl.addFunction('defaultOnChordClick', defaultOnChordClick);