@jbrowse/plugin-linear-genome-view 4.0.2 → 4.0.4

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -11,7 +11,7 @@ const Tooltip = observer(function Tooltip({ model, clientMouseCoord, }) {
     const { featureUnderMouse, featureIdUnderMouse, mouseoverExtraInformation } = model;
     const x = clientMouseCoord[0] + 15;
     const y = clientMouseCoord[1];
-    const contents = useMemo(() => featureUnderMouse || mouseoverExtraInformation
+    const contents = useMemo(() => featureUnderMouse && mouseoverExtraInformation
         ? getConf(model, 'mouseover', {
             feature: featureUnderMouse,
             mouseoverExtraInformation,

package/esm/BaseLinearDisplay/model.d.ts

@@ -139,6 +139,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -195,6 +196,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -248,6 +250,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -529,6 +532,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -585,6 +589,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -638,6 +643,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -864,6 +870,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -920,6 +927,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -973,6 +981,7 @@ export declare const BaseLinearDisplay: import("@jbrowse/mobx-state-tree").IMode
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/BaseLinearDisplay/model.js

@@ -16,7 +16,7 @@ import FeatureDensityMixin from "./models/FeatureDensityMixin.js";
 import TrackHeightMixin from "./models/TrackHeightMixin.js";
 import configSchema from "./models/configSchema.js";
 import BlockState from "./models/serverSideRenderedBlock.js";
-import { fetchFeatureByIdRpc, findSubfeatureById, getTranscripts, hasExonsOrCDS, } from "./util.js";
+import { fetchFeatureByIdRpc, findSubfeatureById, getTranscripts, hasIntrons, } from "./util.js";
 const Tooltip = lazy(() => import("./components/Tooltip.js"));
 const CollapseIntronsDialog = lazy(() => import("./components/CollapseIntronsDialog/CollapseIntronsDialog.js"));
 function stateModelFactory() {
@@ -321,7 +321,7 @@ function stateModelFactory() {
                             session.notify('Copied to clipboard', 'success');
                         },
                     },
-                    ...(hasExonsOrCDS(transcripts)
+                    ...(hasIntrons(transcripts)
                         ? [
                             {
                                 label: 'Collapse introns',
@@ -379,7 +379,7 @@ function stateModelFactory() {
         afterAttach() {
             addDisposer(self, autorun(function blockDefinitionsAutorun() {
                 try {
-                    if (!isAlive(self)) {
+                    if (!isAlive(self) || self.isMinimized) {
                         return;
                     }
                     const view = getContainingView(self);

package/esm/BaseLinearDisplay/util.d.ts

@@ -11,5 +11,6 @@ export declare function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, re
 export declare function findSubfeatureById(feature: Feature, targetId: string): Feature | undefined;
 export declare function featureHasExonsOrCDS(feature: Feature): boolean;
 export declare function hasExonsOrCDS(transcripts: Feature[]): boolean;
+export declare function hasIntrons(transcripts: Feature[]): boolean;
 export declare function getTranscripts(feature?: Feature): Feature[];
 export declare function drawCanvasImageData(canvas: HTMLCanvasElement | null, imageData: ImageBitmap | undefined): boolean;

package/esm/BaseLinearDisplay/util.js

@@ -1,4 +1,4 @@
-import { SimpleFeature } from '@jbrowse/core/util';
+import { SimpleFeature, mergeIntervals } from '@jbrowse/core/util';
 export async function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, rendererType, featureId, parentFeatureId, }) {
     const lookupId = parentFeatureId || featureId;
     const { feature: featureData } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
@@ -38,6 +38,16 @@ export function featureHasExonsOrCDS(feature) {
 export function hasExonsOrCDS(transcripts) {
     return transcripts.some(t => featureHasExonsOrCDS(t));
 }
+export function hasIntrons(transcripts) {
+    const subs = transcripts.flatMap(transcript => transcript
+        .get('subfeatures')
+        ?.filter((f) => f.get('type') === 'exon' || f.get('type') === 'CDS') ?? []);
+    if (subs.length < 2) {
+        return false;
+    }
+    const merged = mergeIntervals(subs.map((f) => ({ start: f.get('start'), end: f.get('end') })), 0);
+    return merged.length > 1;
+}
 export function getTranscripts(feature) {
     if (!feature) {
         return [];

package/esm/LinearBareDisplay/model.d.ts

@@ -134,6 +134,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -190,6 +191,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -243,6 +245,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -524,6 +527,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -580,6 +584,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -633,6 +638,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -859,6 +865,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -915,6 +922,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -968,6 +976,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/LinearBasicDisplay/model.d.ts

@@ -147,6 +147,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -203,6 +204,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -256,6 +258,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -537,6 +540,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -593,6 +597,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -646,6 +651,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -872,6 +878,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -928,6 +935,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -981,6 +989,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1087,7 +1096,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
 } & {
-    readonly activeFilters: any;
+    readonly activeFilters: string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1175,6 +1184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1228,11 +1238,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
     trackMenuItems(): MenuItem[];
+} & {
+    afterAttach(): void;
 } & {
     readonly geneGlyphMode: any;
     readonly subfeatureLabels: any;

package/esm/LinearFeatureDisplay/model.d.ts

@@ -143,6 +143,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -199,6 +200,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -252,6 +254,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -533,6 +536,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -589,6 +593,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -642,6 +647,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -868,6 +874,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -924,6 +931,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -977,6 +985,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1083,7 +1092,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     featureUnderMouseVolatile: Feature | undefined;
 } & {
-    readonly activeFilters: any;
+    readonly activeFilters: string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1171,6 +1180,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1224,11 +1234,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
     trackMenuItems(): MenuItem[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{

package/esm/LinearFeatureDisplay/model.js

@@ -3,8 +3,9 @@ import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { SimpleFeature, getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { cast, getParent, isAlive, types } from '@jbrowse/mobx-state-tree';
+import { addDisposer, cast, getParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import VisibilityIcon from '@mui/icons-material/Visibility';
+import { reaction } from 'mobx';
 import { BaseLinearDisplay } from "../BaseLinearDisplay/index.js";
 const SetMaxHeightDialog = lazy(() => import("./components/SetMaxHeightDialog.js"));
 const AddFiltersDialog = lazy(() => import("./components/AddFiltersDialog.js"));
@@ -245,6 +246,35 @@ function stateModelFactory(configSchema) {
             },
         };
     })
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, reaction(() => self.featureIdUnderMouse, async (featureId) => {
+                if (!featureId) {
+                    self.setFeatureUnderMouse(undefined);
+                    return;
+                }
+                const session = getSession(self);
+                const { rpcManager } = session;
+                const { parentTrack } = self;
+                try {
+                    const sessionId = getRpcSessionId(self);
+                    const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId,
+                        sessionId,
+                        trackInstanceId: parentTrack.id,
+                        rendererType: self.rendererTypeName,
+                    }));
+                    if (isAlive(self) &&
+                        feature &&
+                        self.featureIdUnderMouse === featureId) {
+                        self.setFeatureUnderMouse(new SimpleFeature(feature));
+                    }
+                }
+                catch (e) {
+                }
+            }, { delay: 50, name: 'LinearFeatureDisplayMouseoverReaction' }));
+        },
+    }))
         .postProcessSnapshot(snap => {
         if (!snap) {
             return snap;

package/esm/LinearGenomeView/components/HeaderRegionWidth.js

@@ -12,7 +12,7 @@ const useStyles = makeStyles()({
 });
 const HeaderRegionWidth = observer(function HeaderRegionWidth({ model, }) {
     const { classes } = useStyles();
-    const { coarseTotalBpDisplayStr } = model;
-    return (_jsx(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: coarseTotalBpDisplayStr }));
+    const { effectiveTotalBpDisplayStr } = model;
+    return (_jsx(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: effectiveTotalBpDisplayStr }));
 });
 export default HeaderRegionWidth;

package/esm/LinearGenomeView/components/HeaderZoomControls.js

@@ -26,13 +26,13 @@ function ValueLabelComponent(props) {
 }
 const HeaderZoomControls = observer(function HeaderZoomControls({ model, }) {
     const { classes } = useStyles();
-    const { width, maxBpPerPx, minBpPerPx, bpPerPx } = model;
+    const { width, maxBpPerPx, minBpPerPx, bpPerPx, effectiveBpPerPx } = model;
     const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
     useEffect(() => {
-        setValue(-Math.log2(bpPerPx) * 100);
-    }, [bpPerPx]);
-    const zoomInDisabled = bpPerPx <= minBpPerPx + 0.0001;
-    const zoomOutDisabled = bpPerPx >= maxBpPerPx - 0.0001;
+        setValue(-Math.log2(effectiveBpPerPx) * 100);
+    }, [effectiveBpPerPx]);
+    const zoomInDisabled = effectiveBpPerPx <= minBpPerPx + 0.0001;
+    const zoomOutDisabled = effectiveBpPerPx >= maxBpPerPx - 0.0001;
     return (_jsxs("div", { className: classes.container, children: [_jsx(Tooltip, { title: "Zoom out 2x", children: _jsx("span", { children: _jsx(IconButton, { "data-testid": "zoom_out", disabled: zoomOutDisabled, onClick: () => {
                             model.zoom(bpPerPx * 2);
                         }, children: _jsx(ZoomOut, {}) }) }) }), _jsx(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), valueLabelDisplay: "auto", valueLabelFormat: newValue => `Window size: ${getBpDisplayStr(2 ** (-newValue / 100) * width)}`, slots: {

package/esm/LinearGenomeView/components/MiniControls.js

@@ -20,12 +20,12 @@ const useStyles = makeStyles()(theme => ({
 }));
 const MiniControls = observer(function MiniControls({ model, }) {
     const { classes } = useStyles();
-    const { id, bpPerPx, maxBpPerPx, minBpPerPx, hideHeader } = model;
+    const { id, bpPerPx, maxBpPerPx, minBpPerPx, hideHeader, effectiveBpPerPx } = model;
     const { focusedViewId } = getSession(model);
     return hideHeader ? (_jsx(Paper, { className: classes.background, children: _jsxs(Paper, { className: focusedViewId === id ? classes.focusedBackground : undefined, children: [_jsx(CascadingMenuButton, { menuItems: () => model.menuItems(), children: _jsx(ArrowDown, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_out", onClick: () => {
                         model.zoom(bpPerPx * 2);
-                    }, disabled: bpPerPx >= maxBpPerPx - 0.0001, children: _jsx(ZoomOut, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_in", onClick: () => {
+                    }, disabled: effectiveBpPerPx >= maxBpPerPx - 0.0001, children: _jsx(ZoomOut, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_in", onClick: () => {
                         model.zoom(bpPerPx / 2);
-                    }, disabled: bpPerPx <= minBpPerPx + 0.0001, children: _jsx(ZoomIn, { fontSize: "small" }) })] }) })) : null;
+                    }, disabled: effectiveBpPerPx <= minBpPerPx + 0.0001, children: _jsx(ZoomIn, { fontSize: "small" }) })] }) })) : null;
 });
 export default MiniControls;

package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js

@@ -2,11 +2,13 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { TextField } from '@mui/material';
 export default function AutocompleteTextField({ TextFieldProps, inputBoxVal, params, setInputValue, setCurrentSearch, }) {
     const { helperText, slotProps = {} } = TextFieldProps;
+    const { ref: inputRef, ...restInputProps } = params.InputProps;
+    const { InputProps: _InputProps, ...restParams } = params;
     return (_jsx(TextField, { onBlur: () => {
             setInputValue(inputBoxVal);
-        }, ...params, ...TextFieldProps, size: "small", helperText: helperText, slotProps: {
+        }, ...restParams, ...TextFieldProps, inputRef: inputRef, size: "small", helperText: helperText, slotProps: {
             input: {
-                ...params.InputProps,
+                ...restInputProps,
                 ...slotProps.input,
             },
         }, placeholder: "Search for location", onChange: e => {

package/esm/LinearGenomeView/components/Rubberband.js

@@ -17,10 +17,10 @@ const useStyles = makeStyles()({
 const Rubberband = observer(function Rubberband({ model, ControlComponent = _jsx("div", {}), }) {
     const ref = useRef(null);
     const { classes } = useStyles();
-    const { stickyViewHeaders, rubberbandTop } = model;
+    const { stickyViewHeaders, rubberbandTop, isScalebarRefNameMenuOpen } = model;
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, open, isClick, clickBpOffset, handleMenuItemClick, handleClose, mouseMove, mouseDown, mouseOut, } = useRangeSelect(ref, model);
-    return (_jsxs(_Fragment, { children: [guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                    left: anchorPosition.clientX,
+    return (_jsxs(_Fragment, { children: [guideX !== undefined && !isScalebarRefNameMenuOpen ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                    left: anchorPosition.clientX + 10,
                     top: anchorPosition.clientY,
                 }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: isClick && clickBpOffset
                     ? model.rubberbandClickMenuItems(clickBpOffset)

package/esm/LinearGenomeView/components/Scalebar.d.ts

@@ -6,5 +6,5 @@ interface ScalebarProps {
     style?: React.CSSProperties;
     className?: string;
 }
-declare const Scalebar: React.ForwardRefExoticComponent<ScalebarProps & React.RefAttributes<HTMLDivElement>>;
+declare const Scalebar: ({ model, style, className, ...other }: ScalebarProps) => import("react/jsx-runtime").JSX.Element;
 export default Scalebar;

package/esm/LinearGenomeView/components/Scalebar.js

@@ -1,5 +1,4 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { forwardRef } from 'react';
 import { cx, makeStyles } from '@jbrowse/core/util/tss-react';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -20,14 +19,14 @@ const useStyles = makeStyles()({
         pointerEvents: 'none',
     },
 });
-const Scalebar = observer(forwardRef(function Scalebar2({ model, style, className, ...other }, ref) {
+const Scalebar = observer(function Scalebar({ model, style, className, ...other }) {
     const { classes } = useStyles();
     const { scaleFactor, staticBlocks, offsetPx } = model;
-    return (_jsxs(Paper, { "data-resizer": "true", className: cx(classes.container, className), variant: "outlined", ref: ref, style: { ...style, '--offset-px': `${offsetPx}px` }, ...other, children: [_jsx(Gridlines, { model: model, offset: 1 }), _jsx("div", { className: classes.zoomContainer, style: {
+    return (_jsxs(Paper, { "data-resizer": "true", className: cx(classes.container, className), variant: "outlined", style: { ...style, '--offset-px': `${offsetPx}px` }, ...other, children: [_jsx(Gridlines, { model: model, offset: 1 }), _jsx("div", { className: classes.zoomContainer, style: {
                     transform: scaleFactor !== 1 ? `scaleX(${scaleFactor})` : undefined,
                 }, children: _jsx("div", { className: classes.scalebar, style: {
                         transform: `translateX(calc(${staticBlocks.offsetPx}px - var(--offset-px) - 1px))`,
                         width: staticBlocks.totalWidthPx,
                     }, children: _jsx(ScalebarCoordinateLabels, { model: model }) }) }), _jsx(ScalebarRefNameLabels, { model: model })] }));
-}));
+});
 export default Scalebar;

package/esm/LinearGenomeView/components/ScalebarRefNameLabels.js

@@ -1,4 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { Menu } from '@jbrowse/core/ui';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
@@ -11,6 +13,12 @@ const useStyles = makeStyles()(theme => ({
         lineHeight: 'normal',
         zIndex: 1,
         background: theme.palette.background.paper,
+        cursor: 'pointer',
+        overflow: 'hidden',
+        whiteSpace: 'nowrap',
+        '&:hover': {
+            background: theme.palette.grey[300],
+        },
     },
     b0: {
         left: 0,
@@ -20,6 +28,10 @@ const useStyles = makeStyles()(theme => ({
 const ScalebarRefNameLabels = observer(function ScalebarRefNameLabels({ model, }) {
     const { classes, cx } = useStyles();
     const { staticBlocks, offsetPx, scalebarDisplayPrefix } = model;
+    const [menuState, setMenuState] = useState();
+    useEffect(() => {
+        model.setIsScalebarRefNameMenuOpen(!!menuState);
+    }, [model, menuState]);
     let lastLeftBlock = staticBlocks.blocks.findIndex(b => b.type === 'ContentBlock');
     if (lastLeftBlock < 0) {
         lastLeftBlock = 0;
@@ -31,16 +43,126 @@ const ScalebarRefNameLabels = observer(function ScalebarRefNameLabels({ model, }
     });
     const val = scalebarDisplayPrefix();
     const b0 = staticBlocks.blocks[0];
+    const regionEndPx = new Map();
+    for (const block of staticBlocks.blocks) {
+        if (block.type === 'ContentBlock' && block.regionNumber !== undefined) {
+            const endPx = block.offsetPx + block.widthPx;
+            const current = regionEndPx.get(block.regionNumber);
+            if (current === undefined || endPx > current) {
+                regionEndPx.set(block.regionNumber, endPx);
+            }
+        }
+    }
     return (_jsxs(_Fragment, { children: [b0?.type !== 'ContentBlock' && val ? (_jsx("span", { className: cx(classes.b0, classes.refLabel), children: val })) : null, staticBlocks.map((block, index) => {
-                const { offsetPx: blockOffsetPx, isLeftEndOfDisplayedRegion, key, type, refName, } = block;
+                const { offsetPx: blockOffsetPx, isLeftEndOfDisplayedRegion, key, type, refName, regionNumber, } = block;
                 const last = index === lastLeftBlock;
+                const regEndPx = regionNumber !== undefined ? regionEndPx.get(regionNumber) : undefined;
+                const labelStartPx = last ? offsetPx : blockOffsetPx;
+                const maxWidth = regEndPx !== undefined ? regEndPx - labelStartPx - 2 : undefined;
+                const minLabelWidth = 20;
+                const hasEnoughSpace = maxWidth === undefined || maxWidth >= minLabelWidth;
                 return type === 'ContentBlock' &&
-                    (isLeftEndOfDisplayedRegion || last) ? (_jsxs("span", { style: {
+                    (isLeftEndOfDisplayedRegion || last) &&
+                    hasEnoughSpace ? (_jsxs("span", { style: {
                         left: last
                             ? 'max(0px, calc(-1 * var(--offset-px)))'
                             : `calc(${blockOffsetPx}px - var(--offset-px) - 1px)`,
                         paddingLeft: last ? 0 : 1,
-                    }, className: classes.refLabel, "data-testid": `refLabel-${refName}`, children: [last && val ? `${val}:` : '', refName] }, `refLabel-${key}-${index}`)) : null;
-            })] }));
+                        maxWidth: maxWidth !== undefined && maxWidth > 0 ? maxWidth : undefined,
+                    }, className: classes.refLabel, "data-testid": `refLabel-${refName}`, onMouseDown: () => {
+                        model.setScalebarRefNameClickPending(true);
+                    }, onClick: event => {
+                        model.setScalebarRefNameClickPending(false);
+                        setMenuState({
+                            anchorEl: event.currentTarget,
+                            refName,
+                            regionNumber: regionNumber,
+                        });
+                    }, children: [last && val ? `${val}:` : '', refName] }, `refLabel-${key}-${index}`)) : null;
+            }), menuState ? (_jsx(RefNameMenu, { model: model, menuState: menuState, onClose: () => {
+                    setMenuState(undefined);
+                } })) : null] }));
 });
+function RefNameMenu({ model, menuState, onClose, }) {
+    const { displayedRegions } = model;
+    const { refName, regionNumber } = menuState;
+    const numRegions = displayedRegions.length;
+    function moveRegion(fromIndex, toIndex) {
+        const regions = [...displayedRegions];
+        const [removed] = regions.splice(fromIndex, 1);
+        regions.splice(toIndex, 0, removed);
+        model.setDisplayedRegions(regions);
+    }
+    function removeRegion(index) {
+        const regions = displayedRegions.filter((_, i) => i !== index);
+        model.setDisplayedRegions(regions);
+    }
+    const actionItems = [
+        ...(regionNumber > 0
+            ? [
+                {
+                    label: 'Move left',
+                    onClick: () => {
+                        moveRegion(regionNumber, regionNumber - 1);
+                    },
+                },
+            ]
+            : []),
+        ...(regionNumber < numRegions - 1
+            ? [
+                {
+                    label: 'Move right',
+                    onClick: () => {
+                        moveRegion(regionNumber, regionNumber + 1);
+                    },
+                },
+            ]
+            : []),
+        ...(numRegions > 2 && regionNumber > 0
+            ? [
+                {
+                    label: 'Move to far left',
+                    onClick: () => {
+                        moveRegion(regionNumber, 0);
+                    },
+                },
+            ]
+            : []),
+        ...(numRegions > 2 && regionNumber < numRegions - 1
+            ? [
+                {
+                    label: 'Move to far right',
+                    onClick: () => {
+                        moveRegion(regionNumber, numRegions - 1);
+                    },
+                },
+            ]
+            : []),
+        {
+            label: 'Remove this region from view',
+            onClick: () => {
+                removeRegion(regionNumber);
+            },
+        },
+    ];
+    return (_jsx(Menu, { anchorEl: menuState.anchorEl, open: true, onClose: onClose, onMenuItemClick: (_, callback) => {
+            callback();
+            onClose();
+        }, menuItems: [
+            {
+                label: `Focus on ${refName}`,
+                onClick: () => {
+                    model.navTo({ refName });
+                },
+            },
+            ...(numRegions > 1
+                ? [
+                    {
+                        label: 'Actions',
+                        subMenu: actionItems,
+                    },
+                ]
+                : []),
+        ] }));
+}
 export default ScalebarRefNameLabels;

package/esm/LinearGenomeView/components/TrackLabel.d.ts

@@ -3,5 +3,5 @@ interface Props {
     track: BaseTrackModel;
     className?: string;
 }
-declare const TrackLabel: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
+declare const TrackLabel: ({ track, className }: Props) => import("react/jsx-runtime").JSX.Element;
 export default TrackLabel;

package/esm/LinearGenomeView/components/TrackLabel.js

@@ -1,5 +1,4 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { forwardRef } from 'react';
 import { SanitizedHTML } from '@jbrowse/core/ui';
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
@@ -27,17 +26,17 @@ const useStyles = makeStyles()(theme => ({
         padding: theme.spacing(1),
     },
 }));
-const TrackLabel = observer(forwardRef(function TrackLabel2({ track, className }, ref) {
+const TrackLabel = observer(function TrackLabel({ track, className }) {
     const { classes } = useStyles();
     const view = getContainingView(track);
     const session = getSession(track);
     const { minimized } = track;
     const trackId = track.trackId;
     const trackName = getTrackName(track.configuration, session);
-    return (_jsxs(Paper, { ref: ref, className: cx(className, classes.root), onClick: event => {
+    return (_jsxs(Paper, { className: cx(className, classes.root), onClick: event => {
             event.stopPropagation();
         }, children: [_jsx(TrackLabelDragHandle, { track: track, trackId: trackId, view: view }), _jsx(IconButton, { onClick: () => view.hideTrack(trackId), className: classes.iconButton, title: "close this track", children: _jsx(CloseIcon, { fontSize: "small" }) }), _jsx(Typography, { variant: "body1", component: "span", className: classes.trackName, children: _jsx(SanitizedHTML, { html: [trackName, minimized ? '(minimized)' : '']
                         .filter(f => !!f)
                         .join(' ') }) }), _jsx(TrackLabelMenu, { track: track })] }));
-}));
+});
 export default TrackLabel;

package/esm/LinearGenomeView/components/TracksContainer.js

@@ -25,7 +25,7 @@ const TracksContainer = observer(function TracksContainer({ children, model, })
     const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model);
-    const { stickyViewHeaders, rubberbandTop, showGridlines, showCenterLine } = model;
+    const { stickyViewHeaders, rubberbandTop, showGridlines, showCenterLine, isScalebarRefNameMenuOpen, } = model;
     const ref = useRef(null);
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, open, isClick, clickBpOffset, handleMenuItemClick, handleClose, mouseMove, mouseDown: mouseDown2, } = useRangeSelect(ref, model, true);
     useWheelScroll(ref, model);
@@ -33,7 +33,7 @@ const TracksContainer = observer(function TracksContainer({ children, model, })
     return (_jsxs("div", { ref: ref, "data-testid": "tracksContainer", className: classes.tracksContainer, style: { '--offset-px': `${model.offsetPx}px` }, onMouseDown: event => {
             mouseDown1(event);
             mouseDown2(event);
-        }, onMouseMove: mouseMove, onMouseUp: mouseUp, children: [showGridlines ? _jsx(Gridlines, { model: model }) : null, _jsx(Suspense, { fallback: null, children: showCenterLine ? _jsx(CenterLine, { model: model }) : null }), guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(Suspense, { fallback: null, children: _jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders }) })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+        }, onMouseMove: mouseMove, onMouseUp: mouseUp, children: [showGridlines ? _jsx(Gridlines, { model: model }) : null, _jsx(Suspense, { fallback: null, children: showCenterLine ? _jsx(CenterLine, { model: model }) : null }), guideX !== undefined && !isScalebarRefNameMenuOpen ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(Suspense, { fallback: null, children: _jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders }) })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
                     left: anchorPosition.clientX,
                     top: anchorPosition.clientY,
                 }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: isClick && clickBpOffset

package/esm/LinearGenomeView/components/useRangeSelect.d.ts

@@ -47,6 +47,7 @@ export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement | nul
         end: number;
         reversed?: boolean;
     } | undefined;
+    guideX: number | undefined;
     rubberbandOn: boolean;
     mouseDown: (event: React.MouseEvent<HTMLDivElement>) => void;
     mouseMove: (event: React.MouseEvent<HTMLDivElement>) => void;
@@ -79,6 +80,5 @@ export declare function useRangeSelect(ref: React.RefObject<HTMLDivElement | nul
     numOfBpSelected: number;
     width: number;
     left: number;
-    guideX?: undefined;
 };
 export {};

package/esm/LinearGenomeView/components/useRangeSelect.js

@@ -10,6 +10,7 @@ export function useRangeSelect(ref, model, shiftOnly) {
         setAnchorPosition(undefined);
         setStartX(undefined);
         setCurrentX(undefined);
+        setGuideX(undefined);
     }, []);
     useEffect(() => {
         function computeOffsets(offsetX) {
@@ -34,19 +35,30 @@ export function useRangeSelect(ref, model, shiftOnly) {
                 const { clientX, clientY } = event;
                 const offsetX = getRelativeX(event, ref.current);
                 const isClick = Math.abs(offsetX - startX) <= 3;
+                if (isClick && model.scalebarRefNameClickPending) {
+                    setStartX(undefined);
+                    setCurrentX(undefined);
+                    return;
+                }
+                if (!isClick && model.scalebarRefNameClickPending) {
+                    model.setScalebarRefNameClickPending(false);
+                }
                 setAnchorPosition({
                     offsetX,
                     clientX,
                     clientY,
                     isClick,
                 });
-                if (!isClick) {
+                if (isClick) {
+                    setGuideX(offsetX);
+                }
+                else {
                     const args = computeOffsets(offsetX);
                     if (args) {
                         model.setOffsets(args.leftOffset, args.rightOffset);
                     }
+                    setGuideX(undefined);
                 }
-                setGuideX(undefined);
             }
         }
         if (mouseDragging) {
@@ -63,6 +75,9 @@ export function useRangeSelect(ref, model, shiftOnly) {
         if (shiftOnly && !event.shiftKey) {
             return;
         }
+        if (model.isScalebarRefNameMenuOpen) {
+            return;
+        }
         event.preventDefault();
         event.stopPropagation();
         const relativeX = getRelativeX(event, ref.current);
@@ -70,7 +85,13 @@ export function useRangeSelect(ref, model, shiftOnly) {
         setCurrentX(relativeX);
     }
     function mouseMove(event) {
-        if (shiftOnly) {
+        if (anchorPosition?.isClick === false) {
+            return;
+        }
+        if (mouseDragging) {
+            setGuideX(undefined);
+        }
+        else if (shiftOnly) {
             if (event.shiftKey) {
                 setGuideX(getRelativeX(event, ref.current));
             }
@@ -83,7 +104,9 @@ export function useRangeSelect(ref, model, shiftOnly) {
         }
     }
     function mouseOut() {
-        setGuideX(undefined);
+        if (!anchorPosition?.isClick) {
+            setGuideX(undefined);
+        }
     }
     function handleMenuItemClick(_, callback) {
         callback();
@@ -118,6 +141,7 @@ export function useRangeSelect(ref, model, shiftOnly) {
         open,
         isClick,
         clickBpOffset,
+        guideX,
         rubberbandOn: !isClick,
         mouseDown,
         mouseMove,

package/esm/LinearGenomeView/model.d.ts

@@ -46,11 +46,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     lastTrackDragY: undefined | number;
     volatileError: unknown;
     scaleFactor: number;
+    targetBpPerPx: number | undefined;
     trackRefs: Record<string, HTMLDivElement>;
     coarseDynamicBlocks: BaseBlock[];
     coarseTotalBp: number;
     leftOffset: undefined | BpOffset;
     rightOffset: undefined | BpOffset;
+    isScalebarRefNameMenuOpen: boolean;
+    scalebarRefNameClickPending: boolean;
 } & {
     readonly pinnedTracks: any[];
     readonly unpinnedTracks: any[];
@@ -104,6 +107,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setShowCytobands(flag: boolean): void;
     setWidth(newWidth: number): void;
     setError(error: unknown): void;
+    setIsScalebarRefNameMenuOpen(isOpen: boolean): void;
+    setScalebarRefNameClickPending(pending: boolean): void;
     setHideHeader(b: boolean): void;
     setHideHeaderOverview(b: boolean): void;
     setHideNoTracksActive(b: boolean): void;
@@ -143,6 +148,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setDraggingTrackId(idx?: string): void;
     setLastTrackDragY(y: number): void;
     setScaleFactor(factor: number): void;
+    setTargetBpPerPx(target: number | undefined): void;
     clearView(): void;
     setInit(arg?: InitState): void;
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
@@ -164,6 +170,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly visibleLocStrings: string;
     readonly coarseVisibleLocStrings: string;
     readonly coarseTotalBpDisplayStr: string;
+    readonly effectiveBpPerPx: number;
+    readonly effectiveTotalBp: number;
+    readonly effectiveTotalBpDisplayStr: string;
 } & {
     setCoarseDynamicBlocks(blocks: BlockSet): void;
 } & {
@@ -175,8 +184,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }): Promise<void>;
     navToLocation(parsedLocString: ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
     navToLocations(regions: ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
-    navTo(query: NavLocation): void;
-    navToMultiple(locations: NavLocation[]): void;
+    navTo(query: NavLocation, grow?: number): void;
+    navToMultiple(locations: NavLocation[], grow?: number): void;
 } & {
     rubberBandMenuItems(): MenuItem[];
     bpToPx({ refName, coord, regionNumber, }: {

package/esm/LinearGenomeView/model.js

@@ -19,7 +19,7 @@ import MiniControls from "./components/MiniControls.js";
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, INTER_REGION_PADDING_WIDTH, RESIZE_HANDLE_HEIGHT, SCALE_BAR_HEIGHT, } from "./consts.js";
 import { setupKeyboardHandler } from "./keyboardHandler.js";
 import { buildMenuItems, buildRubberBandMenuItems, buildRubberbandClickMenuItems, rewriteOnClicks, } from "./menuItems.js";
-import { calculateVisibleLocStrings, generateLocations, parseLocStrings, } from "./util.js";
+import { calculateVisibleLocStrings, expandRegion, generateLocations, parseLocStrings, } from "./util.js";
 const SearchResultsDialog = lazy(() => import("./components/SearchResultsDialog.js"));
 export function stateModelFactory(pluginManager) {
     return types
@@ -50,11 +50,14 @@ export function stateModelFactory(pluginManager) {
         lastTrackDragY: undefined,
         volatileError: undefined,
         scaleFactor: 1,
+        targetBpPerPx: undefined,
         trackRefs: {},
         coarseDynamicBlocks: [],
         coarseTotalBp: 0,
         leftOffset: undefined,
         rightOffset: undefined,
+        isScalebarRefNameMenuOpen: false,
+        scalebarRefNameClickPending: false,
     }))
         .views(self => ({
         get pinnedTracks() {
@@ -292,6 +295,12 @@ export function stateModelFactory(pluginManager) {
         setError(error) {
             self.volatileError = error;
         },
+        setIsScalebarRefNameMenuOpen(isOpen) {
+            self.isScalebarRefNameMenuOpen = isOpen;
+        },
+        setScalebarRefNameClickPending(pending) {
+            self.scalebarRefNameClickPending = pending;
+        },
         setHideHeader(b) {
             self.hideHeader = b;
         },
@@ -493,6 +502,9 @@ export function stateModelFactory(pluginManager) {
         setScaleFactor(factor) {
             self.scaleFactor = factor;
         },
+        setTargetBpPerPx(target) {
+            self.targetBpPerPx = target;
+        },
         clearView() {
             this.setDisplayedRegions([]);
             self.tracks.clear();
@@ -523,17 +535,21 @@ export function stateModelFactory(pluginManager) {
         let cancelLastAnimation = () => { };
         function zoom(targetBpPerPx) {
             cancelLastAnimation();
-            self.setScaleFactor(1);
-            self.zoomTo(self.bpPerPx);
-            if ((targetBpPerPx < self.bpPerPx && self.bpPerPx === self.minBpPerPx) ||
-                (targetBpPerPx > self.bpPerPx && self.bpPerPx === self.maxBpPerPx)) {
+            const intendedFactor = targetBpPerPx / self.bpPerPx;
+            const effectiveBase = self.targetBpPerPx ?? self.bpPerPx;
+            let effectiveTarget = effectiveBase * intendedFactor;
+            effectiveTarget = Math.max(self.minBpPerPx, Math.min(self.maxBpPerPx, effectiveTarget));
+            const currentTarget = self.targetBpPerPx ?? self.bpPerPx;
+            if (effectiveTarget === currentTarget) {
                 return;
             }
-            const factor = self.bpPerPx / targetBpPerPx;
-            const [animate, cancelAnimation] = springAnimate(1, factor, self.setScaleFactor, () => {
-                self.zoomTo(targetBpPerPx);
+            self.setTargetBpPerPx(effectiveTarget);
+            const targetScaleFactor = self.bpPerPx / effectiveTarget;
+            const [animate, cancelAnimation] = springAnimate(self.scaleFactor, targetScaleFactor, self.setScaleFactor, () => {
+                self.zoomTo(effectiveTarget);
                 self.setScaleFactor(1);
-            });
+                self.setTargetBpPerPx(undefined);
+            }, 0, 1000, 50);
             cancelLastAnimation = cancelAnimation;
             animate();
         }
@@ -597,6 +613,15 @@ export function stateModelFactory(pluginManager) {
             get coarseTotalBpDisplayStr() {
                 return getBpDisplayStr(self.coarseTotalBp);
             },
+            get effectiveBpPerPx() {
+                return self.targetBpPerPx ?? self.bpPerPx;
+            },
+            get effectiveTotalBp() {
+                return this.effectiveBpPerPx * self.width;
+            },
+            get effectiveTotalBpDisplayStr() {
+                return getBpDisplayStr(this.effectiveTotalBp);
+            },
         };
     })
         .actions(self => ({
@@ -666,10 +691,10 @@ export function stateModelFactory(pluginManager) {
                 self.showAllRegions();
             }
         },
-        navTo(query) {
-            this.navToMultiple([query]);
+        navTo(query, grow) {
+            this.navToMultiple([query], grow);
         },
-        navToMultiple(locations) {
+        navToMultiple(locations, grow) {
             if (locations.some(l => l.start !== undefined && l.end !== undefined && l.start > l.end)) {
                 throw new Error('found start greater than end');
             }
@@ -694,14 +719,21 @@ export function stateModelFactory(pluginManager) {
             if (!lastRegion) {
                 throw new Error(`could not find a region with refName "${lastRefName}"`);
             }
-            const firstStart = firstLocation.start === undefined
+            let firstStart = firstLocation.start === undefined
                 ? firstRegion.start
                 : firstLocation.start;
-            const firstEnd = firstLocation.end === undefined ? firstRegion.end : firstLocation.end;
-            const lastStart = lastLocation.start === undefined
+            let firstEnd = firstLocation.end === undefined ? firstRegion.end : firstLocation.end;
+            let lastStart = lastLocation.start === undefined
                 ? lastRegion.start
                 : lastLocation.start;
-            const lastEnd = lastLocation.end === undefined ? lastRegion.end : lastLocation.end;
+            let lastEnd = lastLocation.end === undefined ? lastRegion.end : lastLocation.end;
+            if (grow) {
+                const expanded = expandRegion(firstStart, lastEnd, grow, firstRegion.start, lastRegion.end);
+                firstStart = expanded.start;
+                firstEnd = expanded.end;
+                lastStart = expanded.start;
+                lastEnd = expanded.end;
+            }
             const firstIndex = self.displayedRegions.findIndex(r => firstRefName === r.refName &&
                 firstStart >= r.start &&
                 firstStart <= r.end &&

package/esm/LinearGenomeView/util.d.ts

@@ -1,5 +1,9 @@
 import type { AssemblyManager, ParsedLocString } from '@jbrowse/core/util';
 import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
+export declare function expandRegion(start: number, end: number, grow: number, minBound?: number, maxBound?: number): {
+    start: number;
+    end: number;
+};
 export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
     majorPitch: number;
     minorPitch: number;
@@ -17,9 +21,9 @@ export declare function generateLocations({ regions, assemblyManager, assemblyNa
 }): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
+    start?: number;
+    end?: number;
     refName: string;
-    start?: number | undefined;
-    end?: number | undefined;
     reversed?: boolean | undefined;
 }[]>;
 export declare function parseLocStrings(input: string, assemblyName: string, isValidRefName: (str: string, assemblyName: string) => boolean): ParsedLocString[];

package/esm/LinearGenomeView/util.js

@@ -1,4 +1,12 @@
 import { assembleLocString, parseLocString } from '@jbrowse/core/util';
+export function expandRegion(start, end, grow, minBound = 0, maxBound = Infinity) {
+    const len = end - start;
+    const margin = len * grow;
+    return {
+        start: Math.max(minBound, start - margin),
+        end: Math.min(maxBound, end + margin),
+    };
+}
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
@@ -74,24 +82,15 @@ export async function generateLocations({ regions, assemblyManager, assemblyName
             throw new Error(`Could not find refName ${refName} in ${asmName}`);
         }
         const { start, end } = region;
-        if (grow && start && end) {
-            const len = end - start;
-            const margin = len * grow;
-            return {
-                ...region,
-                start: Math.max(0, start - margin),
-                end: end + margin,
-                assemblyName: asmName,
-                parentRegion,
-            };
-        }
-        else {
-            return {
-                ...region,
-                assemblyName: asmName,
-                parentRegion,
-            };
-        }
+        const expanded = grow && start !== undefined && end !== undefined
+            ? expandRegion(start, end, grow)
+            : undefined;
+        return {
+            ...region,
+            ...(expanded ? { start: expanded.start, end: expanded.end } : {}),
+            assemblyName: asmName,
+            parentRegion,
+        };
     }));
 }
 export function parseLocStrings(input, assemblyName, isValidRefName) {

package/esm/index.d.ts

@@ -139,6 +139,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -195,6 +196,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -248,6 +250,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -529,6 +532,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & {
@@ -585,6 +589,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             }> | null;
                             readonly adapterConfig: any;
                             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                            readonly isMinimized: boolean;
                             readonly parentDisplay: any;
                             readonly effectiveRpcDriverName: any;
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -638,6 +643,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             }> | null;
                             readonly adapterConfig: any;
                             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                            readonly isMinimized: boolean;
                             readonly parentDisplay: any;
                             readonly effectiveRpcDriverName: any;
                         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -864,6 +870,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & {
@@ -920,6 +927,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             }> | null;
                             readonly adapterConfig: any;
                             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                            readonly isMinimized: boolean;
                             readonly parentDisplay: any;
                             readonly effectiveRpcDriverName: any;
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -973,6 +981,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             }> | null;
                             readonly adapterConfig: any;
                             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                            readonly isMinimized: boolean;
                             readonly parentDisplay: any;
                             readonly effectiveRpcDriverName: any;
                         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "4.0.2",
+  "version": "4.0.4",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -28,8 +28,8 @@
     "file-saver-es": "^2.0.5",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "@jbrowse/product-core": "^4.0.2",
-    "@jbrowse/core": "^4.0.2"
+    "@jbrowse/core": "^4.0.4",
+    "@jbrowse/product-core": "^4.0.4"
   },
   "peerDependencies": {
     "react": ">=18.0.0",