@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/dist/LinearAlignmentsDisplay/model.js

@@ -4,13 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
-// jbrowse
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-// locals
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const alignmentsModel_1 = require("./alignmentsModel");
 const util_1 = require("./util");
 const minDisplayHeight = 20;
@@ -43,110 +41,65 @@ function propagateFilterBy(self) {
         });
     }
 }
-/**
- * #stateModel LinearAlignmentsDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [LinearAlignmentsDisplayMixin](../linearalignmentsdisplaymixin)
- */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearAlignmentsDisplay', models_1.BaseDisplay, (0, alignmentsModel_1.LinearAlignmentsDisplayMixin)(pluginManager, configSchema))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         scrollTop: 0,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setScrollTop(scrollTop) {
             self.scrollTop = scrollTop;
         },
-        /**
-         * #action
-         */
         setSNPCoverageHeight(n) {
             self.snpCovHeight = n;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get height() {
             var _a;
             return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
         },
-        /**
-         * #getter
-         */
         get featureIdUnderMouse() {
             return (self.PileupDisplay.featureIdUnderMouse ||
                 self.SNPCoverageDisplay.featureIdUnderMouse);
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get pileupConf() {
             const conf = (0, configuration_1.getConf)(self, 'pileupDisplay');
             return {
                 ...conf,
                 type: self.lowerPanelType,
-                displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                displayId: `${self.configuration.displayId}_${self.lowerPanelType}_xyz`,
             };
         },
-        /**
-         * #method
-         */
         getFeatureByID(blockKey, id) {
             return self.PileupDisplay.getFeatureByID(blockKey, id);
         },
-        /**
-         * #method
-         */
         searchFeatureByID(id) {
             var _a, _b;
             return (_b = (_a = self.PileupDisplay).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, id);
         },
-        /**
-         * #getter
-         */
         get features() {
             return self.PileupDisplay.features;
         },
-        /**
-         * #getteralignmentsdisplaymodel
-         */
         get DisplayBlurb() {
             var _a;
             return (_a = self.PileupDisplay) === null || _a === void 0 ? void 0 : _a.DisplayBlurb;
         },
-        /**
-         * #getter
-         */
         get sortedBy() {
             return self.PileupDisplay.sortedBy;
         },
-        /**
-         * #getter
-         */
         get coverageConf() {
             const conf = (0, configuration_1.getConf)(self, 'snpCoverageDisplay');
             return {
                 ...conf,
-                displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this
+                displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
             };
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setSNPCoverageDisplay(configuration) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
@@ -154,45 +107,27 @@ function stateModelFactory(pluginManager, configSchema) {
                 height: self.snpCovHeight,
             };
         },
-        /**
-         * #action
-         */
         setFeatureDensityStatsLimit(stats) {
             self.PileupDisplay.setFeatureDensityStatsLimit(stats);
             self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
         },
-        /**
-         * #action
-         */
         setPileupDisplay(configuration) {
             self.PileupDisplay = {
                 type: configuration.type || 'LinearPileupDisplay',
                 configuration,
             };
         },
-        /**
-         * #action
-         */
         setHeight(n) {
             self.heightPreConfig = Math.max(n, minDisplayHeight);
             return self.heightPreConfig;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
             self.PileupDisplay.setFilterBy(filter);
             self.SNPCoverageDisplay.setFilterBy(filter);
         },
-        /**
-         * #action
-         */
         setLowerPanelType(type) {
             self.lowerPanelType = type;
         },
-        /**
-         * #action
-         */
         resizeHeight(distance) {
             const oldHeight = self.height;
             const newHeight = this.setHeight(self.height + distance);
@@ -226,9 +161,6 @@ function stateModelFactory(pluginManager, configSchema) {
                 self.PileupDisplay.setHeight(self.height - self.SNPCoverageDisplay.height);
             }));
         },
-        /**
-         * #action
-         */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await (0, mobx_1.when)(() => !self.PileupDisplay.renderProps().notReady &&
@@ -244,9 +176,6 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         return {
-            /**
-             * #method
-             */
             trackMenuItems() {
                 if (!self.PileupDisplay) {
                     return [];
@@ -281,11 +210,9 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .preProcessSnapshot(snap => {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }
-        // @ts-expect-error
         const { height, ...rest } = snap;
         return { heightPreConfig: height, ...rest };
     });

package/dist/LinearAlignmentsDisplay/util.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function getLowerPanelDisplays(pluginManager: PluginManager): import("@jbrowse/core/pluggableElementTypes").DisplayType[];

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,13 +1,8 @@
-import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import { ColorBy, FilterBy } from '../shared/types';
-/**
- * #stateModel SharedLinearPileupDisplayMixin
- * #category display
- * extends `BaseLinearDisplay`
- */
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export declare function SharedLinearPileupDisplayMixin(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>;
@@ -20,21 +15,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     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, Feature> | undefined;
@@ -58,15 +44,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         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;
-            features: Map<string, 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;
@@ -100,37 +80,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
-    /**
-     * #property
-     */
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    /**
-     * #property
-     */
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    /**
-     * #property
-     */
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 }, {
     rendererTypeName: string;
@@ -221,6 +177,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     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;
 } & {
@@ -261,62 +218,25 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     colorTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
 } & {
-    /**
-     * #action
-     */
     setTagsReady(flag: boolean): void;
-    /**
-     * #action
-     */
     setMaxHeight(n?: number): void;
-    /**
-     * #action
-     */
     setFeatureHeight(n?: number): void;
-    /**
-     * #action
-     */
     setNoSpacing(flag?: boolean): void;
-    /**
-     * #action
-     */
     setColorScheme(colorScheme: ColorBy): void;
-    /**
-     * #action
-     */
     updateColorTagMap(uniqueTag: string[]): void;
-    /**
-     * #action
-     */
     setFeatureUnderMouse(feat?: Feature): void;
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
-    /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
     copyFeatureToClipboard(feature: Feature): void;
-    /**
-     * #action
-     */
     setConfig(conf: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
-    /**
-     * #action
-     */
     setJexlFilters(filters: string[]): void;
 } & {
-    /**
-     * #getter
-     */
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -329,34 +249,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
-    /**
-     * #getter
-     */
     readonly maxHeight: any;
-    /**
-     * #getter
-     */
     readonly featureHeightSetting: any;
-    /**
-     * #getter
-     */
     readonly featureUnderMouse: Feature | undefined;
-    /**
-     * #getter
-     */
     renderReady(): boolean;
-    /**
-     * #getter
-     */
     readonly filters: SerializableFilterChain;
 } & {
-    /**
-     * #getter
-     */
     readonly rendererTypeName: string;
-    /**
-     * #method
-     */
     contextMenuItems(): ({
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -368,33 +267,16 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         icon: typeof ContentCopyIcon;
         onClick: () => void;
     })[];
-    /**
-     * #getter
-     */
     readonly DisplayBlurb: ({ model, }: {
         model: {
-            sortedBy?: {
-                pos: number;
-                refName: number;
-                type: string;
-                tag?: string;
-            };
+            sortedBy?: import("../shared/types").SortedBy;
         };
     }) => import("react").JSX.Element | null;
-    /**
-     * #method
-     */
     renderPropsPre(): any;
-    /**
-     * #method
-     */
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
-    /**
-     * #method
-     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -406,9 +288,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     renderProps(): any;
 } & {
     afterAttach(): void;
-}, {
-    type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -420,21 +300,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     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, Feature> | undefined;
@@ -458,15 +329,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         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;
-            features: Map<string, 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;
@@ -499,12 +364,21 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: string;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+}>>, {
     id: string;
+    type: 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>;