@jbrowse/plugin-alignments 2.10.3 → 2.11.1

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts

@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
     viewType: ViewType;
-}): React.JSX.Element;
+}): React.JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -65,7 +65,7 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return (react_1.default.createElement(react_1.default.Fragment, null, ret.length ? (react_1.default.createElement("div", null,
+    return ret.length ? (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
         error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
         react_1.default.createElement("ul", null, ret.map((arg, index) => {
@@ -82,11 +82,11 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
                         f1.refName,
                         ":",
                         (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
-                        " ->",
                         ' ',
+                        "-> ",
                         f2.refName,
                         ":",
                         (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
-        })))) : null));
+        })))) : null;
 }
 exports.default = LaunchBreakpointSplitViewPanel;

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/dist/BamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'BamAdapter',
@@ -37,4 +37,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = BamAdapterF;

package/dist/CramAdapter/CramTestAdapters.js

@@ -64,6 +64,7 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new simpleFeature_1.default({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/dist/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/dist/CramAdapter/index.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'CramAdapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = CramAdapterF;

package/dist/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/dist/GuessAlignmentsTypes/index.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -52,4 +52,5 @@ exports.default = (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}
+exports.default = GuessAlignmentsTypesF;

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/dist/HtsgetBamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-exports.default = (pluginManager) => {
+function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'HtsgetBamAdapter',
@@ -40,4 +40,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = HtsgetBamAdapterF;

package/dist/LinearAlignmentsDisplay/index.d.ts

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

package/dist/LinearAlignmentsDisplay/index.js

@@ -8,7 +8,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
 const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
-function default_1(pluginManager) {
+function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -22,4 +22,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = LinearAlignmentsDisplayF;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -538,7 +538,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                 }
                 catch (e) {
                     console.error(e);
-                    session.notify(`${e}`, 'error');
+                    session.notifyError(`${e}`, e);
                 }
             }));
         },

package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;
-        } | undefined;
+        };
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
         setFeatureHeight: (arg?: number) => void;
         setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
-        noSpacing?: boolean | undefined;
+        noSpacing?: boolean;
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/dist/LinearPileupDisplay/model.d.ts

@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     configuration: AnyConfigurationSchemaType;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #action
-     */
     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>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
+        extra: import("mobx-state-tree").IType<any, any, any>; /**
+         * #action
+         */
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void; /**
-     * #getter
-     */
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
+     * #getter
+     */
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+     * #method
+     */
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
+    /**
+     * #action
+     * overrides base from SharedLinearPileupDisplay to make sortReady false
+     * since changing feature height destroys the sort-induced layout
+     */
+    setFeatureHeight(n?: number): void;
 } & {
     /**
      * #action

package/dist/LinearPileupDisplay/model.js

@@ -39,14 +39,14 @@ const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
 // locals
 const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
 const mobx_1 = require("mobx");
-// async
+// lzies
 const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
 const ModificationsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByModifications'))));
 /**
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
@@ -153,6 +153,15 @@ function stateModelFactory(configSchema) {
                 tag,
             };
         },
+        /**
+         * #action
+         * overrides base from SharedLinearPileupDisplay to make sortReady false
+         * since changing feature height destroys the sort-induced layout
+         */
+        setFeatureHeight(n) {
+            self.sortReady = false;
+            self.featureHeight = n;
+        },
     }))
         .actions(self => {
         // resets the sort object and refresh whole display on reload

package/dist/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/dist/PileupRPC/index.js

@@ -1,8 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const rpcMethods_1 = require("./rpcMethods");
-exports.default = (pm) => {
+function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
-};
+}
+exports.default = PileupRPCMethodsF;

package/dist/PileupRenderer/components/PileupRendering.d.ts

@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
         type: string;
         pos: number;
         refName: string;
-    } | undefined;
+    };
     colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined;
+        tag?: string;
+    };
     filterBy?: {
         tagFilter?: {
             tag: string;
-        } | undefined;
-    } | undefined;
-    onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
+        };
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
 }) => React.JSX.Element;
 export default PileupRendering;

package/dist/SNPCoverageAdapter/index.d.ts

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

package/dist/SNPCoverageAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-function default_1(pluginManager) {
+function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'SNPCoverageAdapter',
@@ -41,4 +41,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = SNPCoverageAdapterF;

package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts

@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
     viewType: ViewType;
-}): React.JSX.Element;
+}): React.JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js

@@ -40,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return (React.createElement(React.Fragment, null, ret.length ? (React.createElement("div", null,
+    return ret.length ? (React.createElement("div", null,
         React.createElement(Typography, null, "Launch split views with breakend source and target"),
         error ? React.createElement(ErrorMessage, { error: error }) : null,
         React.createElement("ul", null, ret.map((arg, index) => {
@@ -57,10 +57,10 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
                         f1.refName,
                         ":",
                         toLocale(f1.strand === 1 ? f1.end : f1.start),
-                        " ->",
                         ' ',
+                        "-> ",
                         f2.refName,
                         ":",
                         toLocale(f2.strand === 1 ? f2.start : f2.end)))));
-        })))) : null));
+        })))) : null;
 }

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/esm/BamAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'BamAdapter',
@@ -9,4 +9,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./BamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/CramAdapter/CramTestAdapters.js

@@ -56,6 +56,7 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new SimpleFeature({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/esm/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/esm/CramAdapter/index.js

@@ -1,7 +1,7 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 // locals
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./CramAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/esm/GuessAlignmentsTypes/index.js

@@ -1,5 +1,5 @@
 import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -50,4 +50,4 @@ export default (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}

package/esm/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/esm/HtsgetBamAdapter/index.js

@@ -1,6 +1,6 @@
 import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-export default (pluginManager) => {
+export default function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'HtsgetBamAdapter',
@@ -12,4 +12,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/LinearAlignmentsDisplay/index.d.ts

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

package/esm/LinearAlignmentsDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './models/configSchema';
 import modelFactory from './models/model';
 import ReactComponent from './components/AlignmentsDisplay';
-export default function (pluginManager) {
+export default function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -509,7 +509,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                 }
                 catch (e) {
                     console.error(e);
-                    session.notify(`${e}`, 'error');
+                    session.notifyError(`${e}`, e);
                 }
             }));
         },

package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;
-        } | undefined;
+        };
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
         setFeatureHeight: (arg?: number) => void;
         setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
-        noSpacing?: boolean | undefined;
+        noSpacing?: boolean;
     };
     handleClose: () => void;
 }) => React.JSX.Element;

package/esm/LinearPileupDisplay/model.d.ts

@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -96,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     configuration: AnyConfigurationSchemaType;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #action
-     */
     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>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        extra: import("mobx-state-tree").IType<any, any, any>;
+        extra: import("mobx-state-tree").IType<any, any, any>; /**
+         * #action
+         */
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -185,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void; /**
-     * #getter
-     */
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -237,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
-    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
+     * #getter
+     */
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -246,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void; /**
+     * #method
+     */
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
@@ -375,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
+    /**
+     * #action
+     * overrides base from SharedLinearPileupDisplay to make sortReady false
+     * since changing feature height destroys the sort-induced layout
+     */
+    setFeatureHeight(n?: number): void;
 } & {
     /**
      * #action

package/esm/LinearPileupDisplay/model.js

@@ -11,14 +11,14 @@ import SortIcon from '@mui/icons-material/Sort';
 // locals
 import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
 import { observable } from 'mobx';
-// async
+// lzies
 const SortByTagDialog = lazy(() => import('./components/SortByTag'));
 const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
 /**
  * #stateModel LinearPileupDisplay
  * #category display
  * extends
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
  */
 function stateModelFactory(configSchema) {
     return types
@@ -125,6 +125,15 @@ function stateModelFactory(configSchema) {
                 tag,
             };
         },
+        /**
+         * #action
+         * overrides base from SharedLinearPileupDisplay to make sortReady false
+         * since changing feature height destroys the sort-induced layout
+         */
+        setFeatureHeight(n) {
+            self.sortReady = false;
+            self.featureHeight = n;
+        },
     }))
         .actions(self => {
         // resets the sort object and refresh whole display on reload

package/esm/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/esm/PileupRPC/index.js

@@ -1,6 +1,6 @@
 import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, PileupGetReducedFeatures, } from './rpcMethods';
-export default (pm) => {
+export default function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new PileupGetReducedFeatures(pm));
-};
+}

package/esm/PileupRenderer/components/PileupRendering.d.ts

@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
         type: string;
         pos: number;
         refName: string;
-    } | undefined;
+    };
     colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined;
+        tag?: string;
+    };
     filterBy?: {
         tagFilter?: {
             tag: string;
-        } | undefined;
-    } | undefined;
-    onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
+        };
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
 }) => React.JSX.Element;
 export default PileupRendering;

package/esm/SNPCoverageAdapter/index.d.ts

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

package/esm/SNPCoverageAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default function (pluginManager) {
+export default function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'SNPCoverageAdapter',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }