@jbrowse/plugin-sv-inspector 3.7.0 → 4.0.0

package/dist/SvInspectorView/model.js

@@ -1,208 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-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"));
-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');
-    const SpreadsheetModel = SpreadsheetViewType.stateModel;
-    const CircularModel = CircularViewType.stateModel;
-    const minHeight = 400;
-    const defaultHeight = 550;
-    const headerHeight = 52;
-    const circularViewOptionsBarHeight = 52;
-    return mobx_state_tree_1.types
-        .compose('SvInspectorView', models_1.BaseViewModel, mobx_state_tree_1.types.model({
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('SvInspectorView'),
-        height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, defaultHeight),
-        onlyDisplayRelevantRegionsInCircularView: false,
-        spreadsheetView: mobx_state_tree_1.types.optional(SpreadsheetModel, () => SpreadsheetModel.create({
-            type: 'SpreadsheetView',
-            hideVerticalResizeHandle: true,
-        })),
-        circularView: mobx_state_tree_1.types.optional(CircularModel, () => CircularModel.create({
-            type: 'CircularView',
-            hideVerticalResizeHandle: true,
-            hideTrackSelectorButton: true,
-            disableImportForm: true,
-        })),
-    }))
-        .volatile(() => ({
-        width: 800,
-        SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent,
-        CircularViewReactComponent: CircularViewType.ReactComponent,
-        circularViewOptionsBarHeight,
-    }))
-        .views(self => ({
-        get assemblyName() {
-            const { assembly } = self.spreadsheetView;
-            return assembly
-                ? (0, configuration_1.readConfObject)(assembly, 'name')
-                : undefined;
-        },
-        get showCircularView() {
-            var _a;
-            return !!((_a = self.spreadsheetView.spreadsheet) === null || _a === void 0 ? void 0 : _a.rowSet);
-        },
-        get features() {
-            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)) || []);
-        },
-        get featuresAdapterConfigSnapshot() {
-            return {
-                type: 'FromConfigAdapter',
-                features: this.features,
-            };
-        },
-        get featureRefNames() {
-            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)
-                : []);
-        },
-        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',
-                        },
-                    },
-                ],
-            };
-        },
-    }))
-        .actions(self => ({
-        setWidth(newWidth) {
-            self.width = newWidth;
-        },
-        setHeight(newHeight) {
-            self.height = Math.max(newHeight, minHeight);
-            return self.height;
-        },
-        setDisplayedRegions(regions) {
-            self.circularView.setDisplayedRegions(regions);
-        },
-        setOnlyDisplayRelevantRegionsInCircularView(val) {
-            self.onlyDisplayRelevantRegionsInCircularView = val;
-        },
-    }))
-        .views(self => ({
-        menuItems() {
-            return [
-                {
-                    label: 'Return to import form',
-                    icon: FolderOpen_1.default,
-                    onClick: () => {
-                        self.spreadsheetView.displaySpreadsheet(undefined);
-                    },
-                },
-            ];
-        },
-    }))
-        .actions(self => ({
-        resizeHeight(distance) {
-            const oldHeight = self.height;
-            const newHeight = self.setHeight(self.height + distance);
-            return newHeight - oldHeight;
-        },
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.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' }));
-            (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',
-            }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                const { onlyDisplayRelevantRegionsInCircularView, circularView, canonicalFeatureRefNameSet, currentAssembly, } = self;
-                if (!circularView.initialized || !(currentAssembly === null || currentAssembly === void 0 ? void 0 : currentAssembly.regions)) {
-                    return;
-                }
-                else if (onlyDisplayRelevantRegionsInCircularView) {
-                    if (circularView.tracks.length === 1) {
-                        try {
-                            circularView.setDisplayedRegions(structuredClone(currentAssembly.regions.filter(r => canonicalFeatureRefNameSet.has(r.refName))));
-                        }
-                        catch (e) {
-                            console.error(e);
-                            (0, util_1.getSession)(self).notifyError(`${e}`, e);
-                        }
-                    }
-                }
-                else {
-                    circularView.setDisplayedRegions(currentAssembly.regions);
-                }
-            }, { name: 'SvInspectorView displayed regions bind' }));
-            (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;
-                for (const t of circularView.tracks) {
-                    circularView.hideTrack(t.configuration.trackId);
-                }
-                if (assemblyName) {
-                    circularView.addTrackConf(generatedTrackConf, {
-                        assemblyName,
-                    });
-                }
-            }, {
-                name: 'SvInspectorView track configuration binding',
-                fireImmediately: true,
-            }));
-        },
-    }))
-        .postProcessSnapshot(snap => {
-        const { circularView, ...rest } = snap;
-        return rest;
-    });
-}
-exports.default = SvInspectorViewF;

package/dist/index.d.ts

@@ -1,7 +0,0 @@
-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;
-    configure(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,32 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const types_1 = require("@jbrowse/core/util/types");
-const TableChart_1 = __importDefault(require("@mui/icons-material/TableChart"));
-const LaunchSvInspectorView_1 = __importDefault(require("./LaunchSvInspectorView"));
-const SvInspectorView_1 = __importDefault(require("./SvInspectorView"));
-class SvInspectorViewPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'SvInspectorViewPlugin';
-    }
-    install(pluginManager) {
-        (0, SvInspectorView_1.default)(pluginManager);
-        (0, LaunchSvInspectorView_1.default)(pluginManager);
-    }
-    configure(pluginManager) {
-        if ((0, types_1.isAbstractMenuManager)(pluginManager.rootModel)) {
-            pluginManager.rootModel.appendToSubMenu(['Add'], {
-                label: 'SV inspector',
-                icon: TableChart_1.default,
-                onClick: (session) => {
-                    session.addView('SvInspectorView', {});
-                },
-            });
-        }
-    }
-}
-exports.default = SvInspectorViewPlugin;