@jbrowse/plugin-alignments 2.12.0 → 2.12.1

package/dist/shared/fetchChains.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchChains = void 0;
+exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
@@ -21,4 +21,3 @@ async function fetchChains(self) {
     self.setChainData(ret);
     self.setLoading(false);
 }
-exports.fetchChains = fetchChains;

package/dist/shared/index.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FilterModel = exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+exports.FilterModel = void 0;
+exports.getUniqueTagValues = getUniqueTagValues;
+exports.getUniqueModificationValues = getUniqueModificationValues;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -17,7 +19,6 @@ async function getUniqueTagValues(self, colorScheme, blocks, opts) {
     });
     return values;
 }
-exports.getUniqueTagValues = getUniqueTagValues;
 async function getUniqueModificationValues(self, adapterConfig, colorScheme, blocks, opts) {
     const { rpcManager } = (0, util_1.getSession)(self);
     const sessionId = (0, tracks_1.getRpcSessionId)(self);
@@ -30,7 +31,6 @@ async function getUniqueModificationValues(self, adapterConfig, colorScheme, blo
     });
     return values;
 }
-exports.getUniqueModificationValues = getUniqueModificationValues;
 exports.FilterModel = mobx_state_tree_1.types.model({
     flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
     flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),

package/dist/shared/renderSvg.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSvg = void 0;
+exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 // stabilize clipid under test for snapshot
@@ -65,4 +65,3 @@ async function renderSvg(self, opts, cb) {
                 dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
     }
 }
-exports.renderSvg = renderSvg;

package/dist/shared/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.hasPairedReads = void 0;
+exports.hasPairedReads = hasPairedReads;
 function hasPairedReads(features) {
     for (const f of features.chains.values()) {
         if (f[0].flags & 1) {
@@ -9,4 +9,3 @@ function hasPairedReads(features) {
     }
     return false;
 }
-exports.hasPairedReads = hasPairedReads;

package/dist/util.d.ts

@@ -17,7 +17,7 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): boolean;
+export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
 export declare const modificationColors: Record<string, string | undefined>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;

package/dist/util.js

@@ -1,6 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.randomColor = exports.createAutorun = exports.modificationColors = exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.pairMap = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
+exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
+exports.getTag = getTag;
+exports.getTagAlt = getTagAlt;
+exports.getColorWGBS = getColorWGBS;
+exports.fetchSequence = fetchSequence;
+exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+exports.createAutorun = createAutorun;
+exports.randomColor = randomColor;
 const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -11,14 +18,12 @@ function getTag(feature, tag) {
     const tags = feature.get('tags');
     return tags !== undefined ? tags[tag] : feature.get(tag);
 }
-exports.getTag = getTag;
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
     var _a;
     return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
-exports.getTagAlt = getTagAlt;
 // orientation definitions from igv.js, see also
 // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 exports.orientationTypes = {
@@ -78,7 +83,6 @@ function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-exports.getColorWGBS = getColorWGBS;
 // fetches region sequence augmenting by +/- 1bp for CpG on either side of
 // requested region
 async function fetchSequence(region, adapter) {
@@ -94,12 +98,10 @@ async function fetchSequence(region, adapter) {
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-exports.fetchSequence = fetchSequence;
 // has to check underlying C-G (aka CpG) on the reference sequence
 function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
 // adapted from IGV
 // https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
 exports.modificationColors = {
@@ -124,8 +126,6 @@ function createAutorun(self, cb, opts) {
         }
     }, opts));
 }
-exports.createAutorun = createAutorun;
 function randomColor() {
     return `hsl(${Math.random() * 200}, 50%, 50%)`;
 }
-exports.randomColor = randomColor;

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -43,7 +43,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
     afterCreate(): void;

package/esm/BamAdapter/BamAdapter.d.ts

@@ -20,7 +20,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     protected configure(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+        sequenceAdapter?: BaseFeatureDataAdapter;
     }>;
     getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;

package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { BamRecord } from '@gmod/bam';
 import BamAdapter from './BamAdapter';

package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -25,9 +25,7 @@ export default function configModelFactory(pm: PluginManager): import("@jbrowse/
         type: string;
         description: string;
         defaultValue: number;
-    }; /**
-     * #slot
-     */
+    };
     fetchSizeLimit: {
         type: string;
         defaultValue: number;

package/esm/LinearAlignmentsDisplay/models/model.d.ts

@@ -37,7 +37,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & import("mobx-state-tree").IStateTreeNode<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>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -46,8 +46,8 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
         model: {
@@ -58,28 +58,38 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        } & IStateTreeNode<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>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import(
+            /**
+             * #action
+             */
+            "mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree" /**
+             * #getter
+             */).ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree" /**
+             * #getter
+             */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import(
+        /**
+         * #getter
+         */
+        "mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: React.FC<any> | undefined;
-    trackMenuItems(): MenuItem[]; /**
-     * #getter
-     */
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    trackMenuItems(): MenuItem[];
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { Feature } from '@jbrowse/core/util';
@@ -38,7 +37,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -50,9 +49,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -61,11 +60,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -171,8 +168,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -182,9 +179,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined; /**
-             * #property
-             */
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
@@ -199,12 +194,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -217,8 +212,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
-    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
     currStatsBpPerPx: number;
 } & {
     readonly currentBytesRequested: number;
@@ -229,13 +224,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     afterAttach(): void;
 } & {
-    setCurrStatsBpPerPx(n: number): void; /**
-     * #property
-     */
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
@@ -244,8 +237,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    featureIdUnderMouse: undefined | string;
+    contextMenuFeature: undefined | Feature;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -253,7 +246,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -266,8 +259,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
+    setContextMenuFeature(feature?: Feature): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -279,7 +272,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: Feature | undefined;
+    featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
@@ -344,7 +337,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        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<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**
@@ -395,8 +394,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 pos: number;
                 refName: number;
                 type: string;
-                tag?: string | undefined;
-            } | undefined;
+                tag?: string;
+            };
         };
     }) => import("react").JSX.Element | null;
     /**
@@ -454,7 +453,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -466,9 +465,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 error?: unknown;
                 reload: () => void;
                 message: import("react").ReactNode;
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -477,11 +476,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #action
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;

package/esm/LinearPileupDisplay/configSchema.d.ts

@@ -36,9 +36,7 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
-        description: string; /**
-         * #slot
-         */
+        description: string;
         defaultValue: number;
     };
     fetchSizeLimit: {
@@ -50,9 +48,7 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         type: string;
         defaultValue: number;
         description: string;
-    }; /**
-     * #slot
-     */
+    };
     mouseover: {
         type: string;
         description: string;