@jbrowse/react-circular-genome-view2 3.2.0

package/esm/createModel/createModel.js

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+import PluginManager from '@jbrowse/core/PluginManager';
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
+import assemblyManagerFactory, { assemblyConfigSchemaFactory, } from '@jbrowse/core/assemblyManager';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { cast, getSnapshot, types } from 'mobx-state-tree';
+import corePlugins from '../corePlugins';
+import createConfigModel from './createConfigModel';
+import createSessionModel from './createSessionModel';
+import { version } from '../version';
+export default function createModel(runtimePlugins, makeWorkerInstance = () => {
+    throw new Error('no makeWorkerInstance supplied');
+}) {
+    const pluginManager = new PluginManager([...corePlugins, ...runtimePlugins].map(P => new P()));
+    pluginManager.createPluggableElements();
+    const Session = createSessionModel(pluginManager);
+    const assemblyConfigSchema = assemblyConfigSchemaFactory(pluginManager);
+    const assemblyManagerType = assemblyManagerFactory(assemblyConfigSchema, pluginManager);
+    const rootModel = types
+        .model('ReactCircularGenomeView', {
+        config: createConfigModel(pluginManager, assemblyConfigSchema),
+        session: Session,
+        assemblyManager: types.optional(assemblyManagerType, {}),
+        internetAccounts: types.array(pluginManager.pluggableMstType('internet account', 'stateModel')),
+    })
+        .volatile(self => ({
+        error: undefined,
+        adminMode: false,
+        version,
+        rpcManager: new RpcManager(pluginManager, self.config.configuration.rpc, {
+            WebWorkerRpcDriver: {
+                makeWorkerInstance,
+            },
+            MainThreadRpcDriver: {},
+        }),
+        textSearchManager: new TextSearchManager(pluginManager),
+    }))
+        .actions(self => ({
+        setSession(sessionSnapshot) {
+            self.session = cast(sessionSnapshot);
+        },
+        renameCurrentSession(sessionName) {
+            const snapshot = JSON.parse(JSON.stringify(getSnapshot(self.session)));
+            snapshot.name = sessionName;
+            this.setSession(snapshot);
+        },
+        setError(error) {
+            self.error = error;
+        },
+        addInternetAccount(internetAccount) {
+            self.internetAccounts.push(internetAccount);
+        },
+        findAppropriateInternetAccount(location) {
+            const selectedId = location.internetAccountId;
+            if (selectedId) {
+                const selectedAccount = self.internetAccounts.find(a => a.internetAccountId === selectedId);
+                if (selectedAccount) {
+                    return selectedAccount;
+                }
+            }
+            for (const account of self.internetAccounts) {
+                const handleResult = account.handlesLocation(location);
+                if (handleResult) {
+                    return account;
+                }
+            }
+            return null;
+        },
+    }))
+        .views(self => ({
+        get jbrowse() {
+            return self.config;
+        },
+        get pluginManager() {
+            return pluginManager;
+        },
+    }));
+    return { model: rootModel, pluginManager };
+}

package/esm/createModel/createSessionModel.d.ts

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+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
+export default function sessionModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("mobx-state-tree").ISimpleType<string>;
+    margin: import("mobx-state-tree").IType<number | undefined, number, number>;
+} & {
+    drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
+    activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
+    minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+} & {
+    connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            name: {
+                type: string;
+                defaultValue: string;
+                description: string;
+            };
+            assemblyNames: {
+                type: string;
+                defaultValue: never[];
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
+    }, {
+        connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    } & {
+        afterAttach(): void;
+        addTrackConf(trackConf: Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+        addTrackConfs(trackConfs: (Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
+        setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
+        clear(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+} & {
+    view: import("mobx-state-tree").IAnyModelType;
+}, {
+    selection: unknown;
+    hovered: unknown;
+} & {
+    readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
+} & {
+    readonly jbrowse: any;
+    readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    readonly configuration: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly adminMode: boolean;
+    readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+} & {
+    readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
+} & {
+    setSelection(thing: unknown): void;
+    clearSelection(): void;
+    setHovered(thing: unknown): void;
+} & {
+    readonly visibleWidget: any;
+} & {
+    setDrawerPosition(arg: string): void;
+    updateDrawerWidth(drawerWidth: number): number;
+    resizeDrawer(distance: number): number;
+    addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
+    showWidget(widget: any): void;
+    hasWidget(widget: any): boolean;
+    hideWidget(widget: any): void;
+    minimizeWidgetDrawer(): void;
+    showWidgetDrawer(): void;
+    hideAllWidgets(): void;
+    editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    afterAttach(): void;
+} & {
+    readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
+} & {
+    makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
+        name: string;
+        tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
+        configuration: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            name: {
+                type: string;
+                defaultValue: string;
+                description: string;
+            };
+            assemblyNames: {
+                type: string;
+                defaultValue: never[];
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    } & {
+        afterAttach(): void;
+        addTrackConf(trackConf: Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+        addTrackConfs(trackConfs: (Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
+        setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
+        clear(): void;
+    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+        name: import("mobx-state-tree").ISimpleType<string>;
+        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            name: {
+                type: string;
+                defaultValue: string;
+                description: string;
+            };
+            assemblyNames: {
+                type: string;
+                defaultValue: never[];
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
+    }, {
+        connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    } & {
+        afterAttach(): void;
+        addTrackConf(trackConf: Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+        addTrackConfs(trackConfs: (Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
+        setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
+        clear(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
+    breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
+    deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+    addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+    clearConnections(): void;
+} & {
+    queueOfDialogs: [import("@jbrowse/core/util/types").DialogComponentType, unknown][];
+} & {
+    readonly DialogComponent: import("@jbrowse/core/util/types").DialogComponentType | undefined;
+    readonly DialogProps: unknown;
+} & {
+    removeActiveDialog(): void;
+    queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util/types").DialogComponentType, unknown]): void;
+} & {
+    getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
+} & {
+    removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
+} & {
+    readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
+} & {
+    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
+    deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+} & {
+    snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+} & {
+    readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+} & {
+    notify(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
+    notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
+    pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
+    popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
+    removeSnackbarMessage(message: string): void;
+} & {
+    task: undefined;
+} & {
+    readonly version: any;
+    readonly assemblies: any[];
+    readonly assemblyNames: any[];
+    readonly connections: any;
+    readonly assemblyManager: any;
+    readonly views: any[];
+    renderProps(): {
+        theme: any;
+        highResolutionScaling: any;
+    };
+} & {
+    addView(typeName: string, initialState?: {}): any;
+    removeView(): void;
+} & {
+    getTrackActionMenuItems(config: any): {
+        label: string;
+        onClick: () => void;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+    }[];
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type SessionStateModel = ReturnType<typeof sessionModelFactory>;
+export type SessionModel = Instance<SessionStateModel>;

package/esm/createModel/createSessionModel.js

@@ -0,0 +1,76 @@
+import { lazy } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import SnackbarModel from '@jbrowse/core/ui/SnackbarModel';
+import { BaseSessionModel, ConnectionManagementSessionMixin, DialogQueueSessionMixin, DrawerWidgetSessionMixin, ReferenceManagementSessionMixin, TracksManagerSessionMixin, } from '@jbrowse/product-core';
+import InfoIcon from '@mui/icons-material/Info';
+import { getParent, types } from 'mobx-state-tree';
+const AboutDialog = lazy(() => import('./AboutDialog'));
+export default function sessionModelFactory(pluginManager) {
+    return types
+        .compose('ReactCircularGenomeViewSession', BaseSessionModel(pluginManager), DrawerWidgetSessionMixin(pluginManager), ConnectionManagementSessionMixin(pluginManager), DialogQueueSessionMixin(pluginManager), TracksManagerSessionMixin(pluginManager), ReferenceManagementSessionMixin(pluginManager), SnackbarModel())
+        .props({
+        view: pluginManager.getViewType('CircularView').stateModel,
+    })
+        .volatile(() => ({
+        task: undefined,
+    }))
+        .views(self => ({
+        get version() {
+            return getParent(self).version;
+        },
+        get assemblies() {
+            return [getParent(self).config.assembly];
+        },
+        get assemblyNames() {
+            return [getParent(self).config.assemblyName];
+        },
+        get connections() {
+            return getParent(self).config.connections;
+        },
+        get assemblyManager() {
+            return getParent(self).assemblyManager;
+        },
+        get views() {
+            return [self.view];
+        },
+        renderProps() {
+            return {
+                theme: getConf(self, 'theme'),
+                highResolutionScaling: getConf(self, 'highResolutionScaling'),
+            };
+        },
+    }))
+        .actions(self => ({
+        addView(typeName, initialState = {}) {
+            const typeDefinition = pluginManager.getElementType('view', typeName);
+            if (!typeDefinition) {
+                throw new Error(`unknown view type ${typeName}`);
+            }
+            self.view = {
+                ...initialState,
+                type: typeName,
+            };
+            return self.view;
+        },
+        removeView() { },
+    }))
+        .views(self => ({
+        getTrackActionMenuItems(config) {
+            return [
+                {
+                    label: 'About track',
+                    onClick: () => {
+                        self.queueDialog(doneCallback => [
+                            AboutDialog,
+                            { config, handleClose: doneCallback },
+                        ]);
+                    },
+                    icon: InfoIcon,
+                },
+            ];
+        },
+    }));
+}
+function z(x) {
+    return x;
+}

package/esm/createModel/index.d.ts

@@ -0,0 +1,3 @@
+export { default } from './createModel';
+export { default as createSessionModel } from './createSessionModel';
+export { default as createConfigModel } from './createConfigModel';

package/esm/createModel/index.js

@@ -0,0 +1,3 @@
+export { default } from './createModel';
+export { default as createSessionModel } from './createSessionModel';
+export { default as createConfigModel } from './createConfigModel';