@jbrowse/plugin-linear-comparative-view 2.6.2 → 2.7.0

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -86,21 +86,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     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>>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        pos: import("mobx-state-tree").ISimpleType<number>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     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>>;
@@ -115,6 +105,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
             value: import("mobx-state-tree").ISimpleType<string>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 } & {
     /**
      * #property
@@ -250,45 +241,31 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    modificationTagMap: import("mobx").ObservableMap<string, string>; /**
-     * #property
-     */
     featureUnderMouseVolatile: Feature | undefined;
-    currSortBpPerPx: number;
-    modificationsReady: boolean;
-    sortReady: boolean;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
-    setModificationsReady(flag: boolean): void;
     setTagsReady(flag: boolean): void;
-    setSortReady(flag: boolean): void;
-    setCurrSortBpPerPx(n: number): void;
     setMaxHeight(n: number): void;
     setFeatureHeight(n?: number | undefined): void;
     setNoSpacing(flag?: boolean | undefined): void;
     setColorScheme(colorScheme: {
         type: string;
         tag?: string | undefined;
+        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
-    updateModificationColorMap(uniqueModifications: string[]): void;
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature | undefined): void;
     selectFeature(feature: Feature): void;
-    clearSelected(): void;
     copyFeatureToClipboard(feature: Feature): void;
-    toggleSoftClipping(): void;
-    toggleMismatchAlpha(): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
-    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/model").Filter): void;
-} & {
-    reload(): void;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared").IFilter): void;
+    setJexlFilters(filters: string[]): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -298,9 +275,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly mismatchAlphaSetting: any;
     readonly featureUnderMouse: Feature | undefined;
-    readonly renderReady: boolean;
+    renderReady(): boolean;
+    readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): ({
@@ -314,68 +291,42 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
         onClick: () => void;
     })[];
-    readonly DisplayBlurb: (props: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    readonly DisplayBlurb: ({ model, }: {
+        model: {
+            sortedBy?: {
+                pos: number;
+                refName: number;
+                type: string;
+                tag?: string | undefined;
+            } | undefined;
+        };
+    }) => import("react").JSX.Element | null;
     renderPropsPre(): any;
-    renderProps(): any;
-    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 | {
+    colorSchemeSubMenuItems(): {
         label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        type: string;
-        checked: boolean;
         onClick: () => void;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        disabled: boolean;
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-        disabled?: undefined;
-    } | {
+    }[];
+    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">> & {
             muiName: string;
         };
         onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: any;
-        onClick: () => void;
-        icon?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
     })[];
+} & {
+    renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    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;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+    })[];
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LGVSyntenyDisplay/model.js

@@ -114,7 +114,7 @@ async function navToSynteny(feature, self) {
  */
 function stateModelFactory(schema) {
     return mobx_state_tree_1.types
-        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.linearPileupDisplayStateModelFactory)(schema), mobx_state_tree_1.types.model({
+        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.SharedLinearPileupDisplayMixin)(schema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -142,11 +142,30 @@ function stateModelFactory(schema) {
                 ];
             },
         };
+    })
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
+        return {
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Color scheme',
+                        subMenu: [...superColorSchemeSubMenuItems()],
+                    },
+                ];
+            },
+        };
     })
         .actions(self => ({
         afterCreate() {
-            // use color by strand to help indicate inversions better
-            self.setColorScheme({ type: 'strand' });
+            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            if (self.colorBy) {
+                self.setColorScheme({ ...self.colorBy });
+            }
+            else {
+                self.setColorScheme({ type: 'strand' });
+            }
         },
     }));
 }

package/dist/LinearComparativeDisplay/configSchemaF.d.ts

@@ -1,5 +1,5 @@
 /**
  * #config LinearComparativeDisplay
  */
-declare function configSchemaFactory(pluginManager: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+declare function configSchemaFactory(_pluginManager: any): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default configSchemaFactory;

package/dist/LinearComparativeDisplay/configSchemaF.js

@@ -5,7 +5,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 /**
  * #config LinearComparativeDisplay
  */
-function configSchemaFactory(pluginManager) {
+function configSchemaFactory(_pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearComparativeDisplay', {}, {
         explicitlyTyped: true,
         /**

package/dist/LinearComparativeDisplay/stateModelFactory.js

@@ -79,14 +79,14 @@ function stateModelFactory(configSchema) {
                 const newFeatIds = new Set((features === null || features === void 0 ? void 0 : features.map(f => f.id())) || []);
                 let foundNewFeatureNotInExistingMap = false;
                 let foundExistingFeatureNotInNewMap = false;
-                for (let i = 0; i < features.length; i++) {
-                    if (!featIds.has(features[i].id())) {
+                for (const feat of features) {
+                    if (!featIds.has(feat.id())) {
                         foundNewFeatureNotInExistingMap = true;
                         break;
                     }
                 }
-                for (let i = 0; i < existingFeatures.length; i++) {
-                    if (!newFeatIds.has(existingFeatures[i].id())) {
+                for (const existingFeat of existingFeatures) {
+                    if (!newFeatIds.has(existingFeat.id())) {
                         foundExistingFeatureNotInNewMap = true;
                         break;
                     }

package/dist/LinearComparativeView/components/LinearComparativeView.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
 import { LinearComparativeViewModel } from '../model';
 type LCV = LinearComparativeViewModel;
-declare const _default: (props: {
+declare const LinearComparativeView: (props: {
     ExtraButtons?: React.ReactNode;
     model: LCV;
 }) => React.JSX.Element;
-export default _default;
+export default LinearComparativeView;

package/dist/LinearComparativeView/components/LinearComparativeView.js

@@ -91,8 +91,9 @@ const OverlayComparativeView = (0, mobx_react_1.observer)(({ model }) => {
                 })),
                 react_1.default.createElement(Overlays, { model: model })))));
 });
-exports.default = (0, mobx_react_1.observer)(function (props) {
+const LinearComparativeView = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const middle = model.tracks.some(({ displays }) => displays.some((d) => (0, configuration_1.getConf)(d, 'middle')));
     return middle ? (react_1.default.createElement(MiddleComparativeView, { ...props })) : (react_1.default.createElement(OverlayComparativeView, { ...props }));
 });
+exports.default = LinearComparativeView;

package/dist/LinearComparativeView/components/Rubberband.d.ts

@@ -1,9 +1,8 @@
 import React from 'react';
 import { LinearComparativeViewModel } from '../model';
 type LCV = LinearComparativeViewModel;
-declare function Rubberband({ model, ControlComponent, }: {
+declare const LinearComparativeRubberband: ({ model, ControlComponent, }: {
     model: LCV;
-    ControlComponent?: React.ReactElement;
-}): React.JSX.Element;
-declare const _default: typeof Rubberband;
-export default _default;
+    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+}) => React.JSX.Element;
+export default LinearComparativeRubberband;

package/dist/LinearComparativeView/components/Rubberband.js

@@ -65,7 +65,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
         },
     };
 });
-function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
+const LinearComparativeRubberband = (0, mobx_react_1.observer)(function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
     const [startX, setStartX] = (0, react_1.useState)();
     const [currentX, setCurrentX] = (0, react_1.useState)();
     // clientX and clientY used for anchorPosition for menu
@@ -199,5 +199,5 @@ function Rubberband({ model, ControlComponent = react_1.default.createElement("d
                 left: anchorPosition.clientX,
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
-}
-exports.default = (0, mobx_react_1.observer)(Rubberband);
+});
+exports.default = LinearComparativeRubberband;

package/dist/LinearComparativeView/model.d.ts

@@ -62,12 +62,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -91,7 +89,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -108,7 +106,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -210,6 +208,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }, {

package/dist/LinearComparativeView/model.js

@@ -140,13 +140,16 @@ function stateModelFactory(pluginManager) {
         // automatically removes session assemblies associated with this view
         // e.g. read vs ref
         beforeDestroy() {
+            var _a;
             const session = (0, util_1.getSession)(self);
-            self.assemblyNames.forEach(asm => session.removeTemporaryAssembly(asm));
+            for (const name of self.assemblyNames) {
+                (_a = session.removeTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, name);
+            }
         },
         onSubviewAction(actionName, path, args) {
             self.views.forEach(view => {
                 const ret = (0, mobx_state_tree_1.getPath)(view);
-                if (ret.lastIndexOf(path) !== ret.length - path.length) {
+                if (!ret.endsWith(path)) {
                     // @ts-expect-error
                     view[actionName](args === null || args === void 0 ? void 0 : args[0]);
                 }

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -93,6 +93,7 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
         })();
     }, [preFeature, track]);
     function onSubmit() {
+        var _a;
         try {
             if (!primaryFeature) {
                 return;
@@ -154,7 +155,7 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
                 end: f.end + windowSize,
                 assemblyName: trackAssembly,
             })));
-            session.addTemporaryAssembly({
+            (_a = session.addTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, {
                 name: `${readAssembly}`,
                 sequence: {
                     type: 'ReferenceSequenceTrack',

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -62,8 +62,7 @@ function doAfterAttach(self) {
         }));
         const map = [];
         const feats = self.features || [];
-        for (let i = 0; i < feats.length; i++) {
-            const f = feats[i];
+        for (const f of feats) {
             const mate = f.get('mate');
             let f1s = f.get('start');
             let f1e = f.get('end');

package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearSyntenyDisplayModel } from '../model';
-declare const _default: ({ model, }: {
+declare const LinearSyntenyRendering: ({ model, }: {
     model: LinearSyntenyDisplayModel;
 }) => React.JSX.Element;
-export default _default;
+export default LinearSyntenyRendering;

package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js

@@ -32,7 +32,7 @@ const util_1 = require("@jbrowse/core/util");
 // locals
 const SyntenyTooltip_1 = __importDefault(require("./SyntenyTooltip"));
 const drawSynteny_1 = require("../drawSynteny");
-exports.default = (0, mobx_react_1.observer)(function LinearSyntenyRendering({ model, }) {
+const LinearSyntenyRendering = (0, mobx_react_1.observer)(function ({ model, }) {
     const highResolutionScaling = 1;
     const view = (0, util_1.getContainingView)(model);
     const height = view.middleComparativeHeight;
@@ -157,3 +157,4 @@ exports.default = (0, mobx_react_1.observer)(function LinearSyntenyRendering({ m
             }, width: width, height: height }),
         model.mouseoverId && tooltip && currX && currY ? (react_1.default.createElement(SyntenyTooltip_1.default, { x: currX, y: currY, title: tooltip })) : null));
 });
+exports.default = LinearSyntenyRendering;

package/dist/LinearSyntenyDisplay/drawSynteny.js

@@ -43,8 +43,7 @@ function drawRef(model, ctx1, ctx3) {
     // call, a separate loop below draws larger boxes
     ctx1.fillStyle = colorMap.M;
     ctx1.strokeStyle = colorMap.M;
-    for (let i = 0; i < featPos.length; i++) {
-        const { p11, p12, p21, p22 } = featPos[i];
+    for (const { p11, p12, p21, p22 } of featPos) {
         const x11 = p11.offsetPx - offsets[0];
         const x12 = p12.offsetPx - offsets[0];
         const x21 = p21.offsetPx - offsets[1];
@@ -74,8 +73,7 @@ function drawRef(model, ctx1, ctx3) {
     // ctx.stroke once is much more efficient than calling stroke() many times
     ctx1.fillStyle = colorMap.M;
     ctx1.strokeStyle = colorMap.M;
-    for (let i = 0; i < featPos.length; i++) {
-        const { p11, p12, p21, p22, f, cigar } = featPos[i];
+    for (const { p11, p12, p21, p22, f, cigar } of featPos) {
         const x11 = p11.offsetPx - offsets[0];
         const x12 = p12.offsetPx - offsets[0];
         const x21 = p21.offsetPx - offsets[1];

package/dist/LinearSyntenyView/components/ImportCustomTrack.d.ts

@@ -2,7 +2,7 @@ import React from 'react';
 import { SnapshotIn } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 type Conf = SnapshotIn<AnyConfigurationModel>;
-declare const OpenTrack: ({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }: {
+declare const OpenTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
     sessionTrackData: Conf;
     assembly1: string;
     assembly2: string;

package/dist/LinearSyntenyView/components/ImportCustomTrack.js

@@ -99,7 +99,7 @@ function getAdapter({ radioOption, assembly1, assembly2, fileLocation, bed1Locat
         throw new Error('Unknown type');
     }
 }
-const OpenTrack = (0, mobx_react_1.observer)(({ sessionTrackData, assembly1, assembly2, setSessionTrackData, }) => {
+const OpenTrack = (0, mobx_react_1.observer)(({ assembly1, assembly2, setSessionTrackData, }) => {
     const [bed2Location, setBed2Location] = (0, react_1.useState)();
     const [bed1Location, setBed1Location] = (0, react_1.useState)();
     const [fileLocation, setFileLocation] = (0, react_1.useState)();

package/dist/LinearSyntenyView/components/ImportForm.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearSyntenyViewModel } from '../model';
-declare const _default: ({ model, }: {
+declare const LinearSyntenyViewImportForm: ({ model, }: {
     model: LinearSyntenyViewModel;
 }) => React.JSX.Element;
-export default _default;
+export default LinearSyntenyViewImportForm;

package/dist/LinearSyntenyView/components/ImportForm.js

@@ -62,7 +62,7 @@ function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData,
         choice === 'custom' ? (react_1.default.createElement(ImportCustomTrack_1.default, { setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, assembly2: assembly2, assembly1: assembly1 })) : null,
         choice === 'tracklist' ? (react_1.default.createElement(ImportSyntenyTrackSelector_1.default, { model: model, assembly1: assembly1, assembly2: assembly2, setShowTrackId: setShowTrackId })) : null));
 }
-exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { assemblyNames } = session;
@@ -124,3 +124,4 @@ exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
                                 react_1.default.createElement(material_1.Button, { onClick: onOpenClick, variant: "contained", color: "primary" }, "Launch"))))),
                 react_1.default.createElement(TrackSelector, { setShowTrackId: setShowTrackId, assembly2: assembly2, assembly1: assembly1, setSessionTrackData: setSessionTrackData, sessionTrackData: sessionTrackData, model: model })))));
 });
+exports.default = LinearSyntenyViewImportForm;

package/dist/LinearSyntenyView/model.d.ts

@@ -73,12 +73,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -102,7 +100,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -119,7 +117,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -221,6 +219,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
@@ -323,12 +323,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -352,7 +350,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -369,7 +367,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -471,6 +469,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -511,12 +511,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
         draggingTrackId: string | undefined;
-        volatileError: Error | undefined;
+        volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
-        trackRefs: {
-            [key: string]: HTMLDivElement;
-        };
+        trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
         leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
@@ -540,7 +538,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         readonly totalBp: number;
         readonly maxBpPerPx: number;
         readonly minBpPerPx: number;
-        readonly error: string | Error;
+        readonly error: {};
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly displayedRegionsTotalPx: number;
@@ -557,7 +555,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
-        setError(error: Error | undefined): void;
+        setError(error: unknown): void;
         toggleHeader(): void;
         toggleHeaderOverview(): void;
         toggleNoTracksActive(): void;
@@ -659,6 +657,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             end: number;
             reversed: boolean;
         } | undefined;
+    } & {
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
     closeView(): void;
     setMiddleComparativeHeight(n: number): number;

package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -5,8 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
+const util_1 = require("@jbrowse/core/util");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }
 exports.default = SVGBackground;

package/dist/SyntenyTrack/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 registerSyntenyTrack(pluginManager: PluginManager): void;