@jbrowse/plugin-sequence 2.17.0 → 3.0.0

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -1,8 +1,4 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export declare function modelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -15,23 +11,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree" /**
-             * #property
-             */).ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -49,23 +34,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement /**
-             * #method
-             */;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -193,14 +170,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -227,70 +205,28 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
-    /**
-     * #property
-     */
     rowHeight: number;
 } & {
-    /**
-     * #getter
-     */
     readonly sequenceType: any;
-    /**
-     * #getter
-     * showReverse setting, it is NOT disabled for non-dna sequences
-     */
     readonly showForwardActual: boolean;
-    /**
-     * #getter
-     * showReverse setting, is disabled for non-dna sequences
-     */
     readonly showReverseActual: boolean;
-    /**
-     * #getter
-     * showTranslation setting is disabled for non-dna sequences
-     */
     readonly showTranslationActual: boolean;
 } & {
-    /**
-     * #getter
-     */
     readonly sequenceHeight: number;
 } & {
-    /**
-     * #method
-     */
     renderProps(): any;
 } & {
-    /**
-     * #method
-     */
     regionCannotBeRendered(): "Zoom in to see sequence" | undefined;
-    /**
-     * #getter
-     */
     readonly rendererTypeName: any;
 } & {
-    /**
-     * #action
-     */
     toggleShowForward(): void;
-    /**
-     * #action
-     */
     toggleShowReverse(): void;
-    /**
-     * #action
-     */
     toggleShowTranslation(): void;
     afterAttach(): void;
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): {
         label: string;
         type: string;
@@ -311,21 +247,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -343,23 +270,15 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement /**
-             * #method
-             */;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -396,8 +315,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     type: string;
     id: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    heightPreConfig: number | undefined;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/esm/LinearReferenceSequenceDisplay/model.js

@@ -1,76 +1,36 @@
-import { addDisposer, types } from 'mobx-state-tree';
-import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
-import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
-import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { getContainingTrack, getContainingView } from '@jbrowse/core/util';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import { autorun } from 'mobx';
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
+import { addDisposer, types } from 'mobx-state-tree';
 export function modelFactory(configSchema) {
     return types
         .compose('LinearReferenceSequenceDisplay', BaseLinearDisplay, types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearReferenceSequenceDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         showForward: true,
-        /**
-         * #property
-         */
         showReverse: true,
-        /**
-         * #property
-         */
         showTranslation: true,
     }))
         .volatile(() => ({
-        /**
-         * #property
-         */
         rowHeight: 15,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get sequenceType() {
             return getConf(getContainingTrack(self), 'sequenceType');
         },
-        /**
-         * #getter
-         * showReverse setting, it is NOT disabled for non-dna sequences
-         */
         get showForwardActual() {
             return self.showForward;
         },
-        /**
-         * #getter
-         * showReverse setting, is disabled for non-dna sequences
-         */
         get showReverseActual() {
             return this.sequenceType === 'dna' ? self.showReverse : false;
         },
-        /**
-         * #getter
-         * showTranslation setting is disabled for non-dna sequences
-         */
         get showTranslationActual() {
             return this.sequenceType === 'dna' ? self.showTranslation : false;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get sequenceHeight() {
             const { rowHeight, showTranslationActual, showReverseActual, showForwardActual, } = self;
             const r1 = showReverseActual && showTranslationActual ? rowHeight * 3 : 0;
@@ -84,9 +44,6 @@ export function modelFactory(configSchema) {
         .views(self => {
         const { renderProps: superRenderProps } = self;
         return {
-            /**
-             * #method
-             */
             renderProps() {
                 const { rpcDriverName, showForwardActual, showReverseActual, showTranslationActual, rowHeight, sequenceHeight, sequenceType, } = self;
                 return {
@@ -105,36 +62,21 @@ export function modelFactory(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #method
-         */
-        regionCannotBeRendered( /* region */) {
+        regionCannotBeRendered() {
             const view = getContainingView(self);
             return view.bpPerPx > 3 ? 'Zoom in to see sequence' : undefined;
         },
-        /**
-         * #getter
-         */
         get rendererTypeName() {
             return self.configuration.renderer.type;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         toggleShowForward() {
             self.showForward = !self.showForward;
         },
-        /**
-         * #action
-         */
         toggleShowReverse() {
             self.showReverse = !self.showReverse;
         },
-        /**
-         * #action
-         */
         toggleShowTranslation() {
             self.showTranslation = !self.showTranslation;
         },
@@ -151,9 +93,6 @@ export function modelFactory(configSchema) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         trackMenuItems() {
             return [
                 ...(self.sequenceType === 'dna'

package/esm/ReferenceSequenceTrack/configSchema.d.ts

@@ -1,60 +1,34 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * configuration for track adapter
-     */
     adapter: import("mobx-state-tree").IAnyModelType;
-    /**
-     * #slot
-     * configuration for the displays e.g. LinearReferenceSequenceDisplay
-     */
     displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    /**
-     * #slot
-     */
     name: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     sequenceType: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     description: {
         description: string;
         type: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     metadata: {
         type: string;
         description: string;
         defaultValue: {};
     };
     formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot formatAbout.config
-         */
         config: {
             type: string;
             description: string;
             defaultValue: {};
             contextVariable: string[];
         };
-        /**
-         * #slot formatAbout.hideUris
-         */
         hideUris: {
             type: string;
             defaultValue: boolean;

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,70 +1,37 @@
-import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-// Note: this is primarily a copy of createBaseTrackConfig, except with a
-// subset of the config slots, to avoid including fields that don't make sense
-// for the ReferenceSequenceTrack
-/**
- * #config ReferenceSequenceTrack
- * used to display base level DNA sequence tracks
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { types } from 'mobx-state-tree';
+function x() { }
 export function createReferenceSeqTrackConfig(pluginManager) {
     return ConfigurationSchema('ReferenceSequenceTrack', {
-        /**
-         * #slot
-         * configuration for track adapter
-         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        /**
-         * #slot
-         * configuration for the displays e.g. LinearReferenceSequenceDisplay
-         */
         displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
-        /**
-         * #slot
-         */
         name: {
             type: 'string',
             description: 'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
             defaultValue: '',
         },
-        /**
-         * #slot
-         */
         sequenceType: {
             type: 'string',
             description: 'either dna or pep',
             defaultValue: 'dna',
         },
-        /**
-         * #slot
-         */
         description: {
             description: 'a description of the track',
             type: 'string',
             defaultValue: '',
         },
-        /**
-         * #slot
-         */
         metadata: {
             type: 'frozen',
             description: 'anything to add about this track',
             defaultValue: {},
         },
         formatAbout: ConfigurationSchema('FormatAbout', {
-            /**
-             * #slot formatAbout.config
-             */
             config: {
                 type: 'frozen',
                 description: 'formats configuration in about dialog',
                 defaultValue: {},
                 contextVariable: ['config'],
             },
-            /**
-             * #slot formatAbout.hideUris
-             */
             hideUris: {
                 type: 'boolean',
                 defaultValue: false,
@@ -76,9 +43,6 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             const displayTypes = new Set();
             const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
-                // Gets the displays on the track snapshot and the possible displays
-                // from the track type and adds any missing possible displays to the
-                // snapshot
                 displays.forEach((d) => d && displayTypes.add(d.type));
                 const trackType = pluginManager.getTrackType(snap.type);
                 trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes.forEach(displayType => {
@@ -92,10 +56,6 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
-        /**
-         * #identifier
-         * all tracks have a globally unique 'trackId'
-         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/esm/ReferenceSequenceTrack/index.d.ts

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

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2, revcom } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
-import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     async configure() {
         var _a;

package/esm/SequenceSearchAdapter/configSchema.d.ts

@@ -1,36 +1,21 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     search: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         defaultValue: null;
     };
-    /**
-     * #slot
-     */
     searchForward: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     searchReverse: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     caseInsensitive: {
         type: string;
         defaultValue: boolean;

package/esm/SequenceSearchAdapter/configSchema.js

@@ -1,41 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config SequenceSearchAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('SequenceSearchAdapter', {
-    /**
-     * #slot
-     */
     search: {
         type: 'string',
         defaultValue: '',
         description: 'Search string or regex to search for',
     },
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: 'frozen',
         defaultValue: null,
     },
-    /**
-     * #slot
-     */
     searchForward: {
         type: 'boolean',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     searchReverse: {
         type: 'boolean',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     caseInsensitive: {
         type: 'boolean',
         defaultValue: true,

package/esm/SequenceSearchAdapter/index.d.ts

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

package/esm/SequenceSearchAdapter/index.js

@@ -1,13 +1,15 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default function SequenceSearchAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'SequenceSearchAdapter',
-        displayName: 'Sequence search adapter',
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        configSchema,
-        getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'SequenceSearchAdapter',
+            displayName: 'Sequence search adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema,
+            getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
+        });
+    });
 }