@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -1,49 +1,51 @@
 import type React from 'react';
-import type { ChainData } from '../shared/fetchChains';
-import type { ColorBy, FilterBy } from '../shared/types';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Instance } from 'mobx-state-tree';
-declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+import type { ExportSvgDisplayOptions, LegendItem } from '@jbrowse/plugin-linear-genome-view';
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
 } & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
 } & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
+    filterBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined>;
+    colorBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined>;
+} & {
+    lineWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    jitter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    drawInter: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawLongRange: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
     configuration: AnyConfigurationSchemaType;
-    lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    jitter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    drawInter: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawLongRange: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 }, {
     rendererTypeName: string;
     error: unknown;
-    message: string | undefined;
+    statusMessage: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -52,30 +54,142 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any;
+    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly parentDisplay: any;
+    readonly effectiveRpcDriverName: any;
+} & {
     renderProps(): any;
+    renderingProps(): {
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    };
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string): void;
+    setStatusMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -110,48 +224,85 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    readonly statsReadyAndRegionNotTooLarge: boolean;
+    readonly featureDensityStatsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
-    chainData: ChainData | undefined;
     lastDrawnOffsetPx: number | undefined;
-    lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
+    renderingImageData: ImageBitmap | undefined;
+    renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
+    statusMessage: string | undefined;
 } & {
-    readonly colorBy: any;
-    readonly filterBy: any;
+    readonly drawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
-    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
-    reload(): void;
     setRef(ref: HTMLCanvasElement | null): void;
+    setRenderingImageData(imageData: ImageBitmap | undefined): void;
+    setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
+    setStatusMessage(msg?: string): void;
+} & {
+    beforeDestroy(): void;
+} & {
+    chainData: import("../shared/types.ts").ChainData | undefined;
+    lastDrawnBpPerPx: number;
+} & {
+    setLastDrawnBpPerPx(n: number): void;
     setColorScheme(colorBy: {
         type: string;
     }): void;
-    setChainData(args: ChainData): void;
+    setChainData(args: import("../shared/types.ts").ChainData): void;
+    setFilterBy(filter: import("../shared/types.ts").FilterBy): void;
+} & {
     setDrawInter(f: boolean): void;
     setDrawLongRange(f: boolean): void;
-    setFilterBy(filter: FilterBy): void;
     setLineWidth(n: number): void;
     setJitter(n: number): void;
 } & {
-    readonly drawn: boolean;
     readonly lineWidthSetting: any;
     readonly jitterVal: number;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
+} & {
+    setShowLegend(s: boolean): void;
+    reload(): void;
+} & {
+    legendItems(): LegendItem[];
+    svgLegendWidth(): number;
 } & {
     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 | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: ({
+            label: string;
+            type: "subMenu";
+            subMenu: ({
+                label: string;
+                onClick: () => void;
+                type?: undefined;
+            } | {
+                type: "divider";
+                label?: undefined;
+                onClick?: undefined;
+            })[] | {
+                label: string;
+            }[];
+        } | {
+            label: string;
+            onClick: () => void;
+        })[];
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-        subMenu?: undefined;
-        type?: undefined;
-        checked?: undefined;
     } | {
         label: string;
         subMenu: {
@@ -160,37 +311,42 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             label: string;
             onClick: () => void;
         }[];
-        icon?: undefined;
-        onClick?: undefined;
         type?: undefined;
-        checked?: undefined;
     } | {
         label: string;
         type: string;
-        checked: boolean;
-        onClick: () => void;
-        icon?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
         subMenu: {
             label: string;
+            type: string;
+            checked: boolean | undefined;
             onClick: () => void;
         }[];
-        onClick?: undefined;
-        type?: undefined;
-        checked?: undefined;
     })[];
-} & {
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<React.ReactNode>;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<React.ReactNode>;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    filterBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined>;
+    colorBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined>;
+} & {
+    lineWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    jitter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    drawInter: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawLongRange: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+}>>;
 export type LinearReadArcsDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearReadArcsDisplayModel = Instance<LinearReadArcsDisplayStateModel>;
 export default stateModelFactory;

package/esm/LinearReadArcsDisplay/model.js

@@ -1,94 +1,40 @@
-import { lazy } from 'react';
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
-import { getSession } from '@jbrowse/core/util';
+import { types } from '@jbrowse/mobx-state-tree';
 import { FeatureDensityMixin, TrackHeightMixin, } from '@jbrowse/plugin-linear-genome-view';
-import FilterListIcon from '@mui/icons-material/ClearAll';
-import PaletteIcon from '@mui/icons-material/Palette';
-import { types } from 'mobx-state-tree';
-const FilterByTagDialog = lazy(() => import('../shared/components/FilterByTagDialog'));
+import { LinearReadArcsDisplaySettingsMixin } from "../shared/LinearReadArcsDisplaySettingsMixin.js";
+import { LinearReadDisplayBaseMixin } from "../shared/LinearReadDisplayBaseMixin.js";
+import { calculateSvgLegendWidth, getReadDisplayLegendItems, } from "../shared/legendUtils.js";
+import { getColorSchemeMenuItem, getFilterByMenuItem, } from "../shared/menuItems.js";
 function stateModelFactory(configSchema) {
     return types
-        .compose('LinearReadArcsDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
+        .compose('LinearReadArcsDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), LinearReadDisplayBaseMixin(), LinearReadArcsDisplaySettingsMixin(), types.model({
         type: types.literal('LinearReadArcsDisplay'),
         configuration: ConfigurationReference(configSchema),
-        lineWidth: types.maybe(types.number),
-        jitter: types.maybe(types.number),
-        colorBySetting: types.frozen(),
-        filterBySetting: types.frozen(),
-        drawInter: true,
-        drawLongRange: true,
-    }))
-        .volatile(() => ({
-        loading: false,
-        chainData: undefined,
-        lastDrawnOffsetPx: undefined,
-        lastDrawnBpPerPx: 0,
-        ref: null,
+        showLegend: types.maybe(types.boolean),
     }))
         .views(self => ({
         get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'colorBy');
+            return self.colorBySetting ?? getConf(self, 'colorBy');
         },
         get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : getConf(self, 'filterBy');
+            return self.filterBySetting ?? getConf(self, 'filterBy');
         },
     }))
         .actions(self => ({
-        setLastDrawnOffsetPx(n) {
-            self.lastDrawnOffsetPx = n;
-        },
-        setLastDrawnBpPerPx(n) {
-            self.lastDrawnBpPerPx = n;
-        },
-        setLoading(f) {
-            self.loading = f;
+        setShowLegend(s) {
+            self.showLegend = s;
         },
         reload() {
             self.error = undefined;
         },
-        setRef(ref) {
-            self.ref = ref;
-        },
-        setColorScheme(colorBy) {
-            self.colorBySetting = {
-                ...colorBy,
-            };
-        },
-        setChainData(args) {
-            self.chainData = args;
-        },
-        setDrawInter(f) {
-            self.drawInter = f;
-        },
-        setDrawLongRange(f) {
-            self.drawLongRange = f;
-        },
-        setFilterBy(filter) {
-            self.filterBySetting = {
-                ...filter,
-            };
-        },
-        setLineWidth(n) {
-            self.lineWidth = n;
-        },
-        setJitter(n) {
-            self.jitter = n;
-        },
     }))
         .views(self => ({
-        get drawn() {
-            return self.lastDrawnOffsetPx !== undefined;
-        },
-        get lineWidthSetting() {
-            var _a;
-            return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
+        legendItems() {
+            return getReadDisplayLegendItems(self.colorBy);
         },
-        get jitterVal() {
-            var _a;
-            return (_a = self.jitter) !== null && _a !== void 0 ? _a : getConf(self, 'jitter');
+        svgLegendWidth() {
+            return self.showLegend ? calculateSvgLegendWidth(this.legendItems()) : 0;
         },
     }))
         .views(self => {
@@ -97,22 +43,20 @@ function stateModelFactory(configSchema) {
             renderProps() {
                 return {
                     ...superRenderProps(),
-                    notReady: !self.chainData,
+                    notReady: false,
+                    filterBy: self.filterBy,
+                    colorBy: self.colorBy,
+                    drawInter: self.drawInter,
+                    drawLongRange: self.drawLongRange,
+                    lineWidth: self.lineWidthSetting,
+                    jitter: self.jitterVal,
+                    height: self.height,
                 };
             },
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
-                    {
-                        label: 'Filter by',
-                        icon: FilterListIcon,
-                        onClick: () => {
-                            getSession(self).queueDialog(handleClose => [
-                                FilterByTagDialog,
-                                { model: self, handleClose },
-                            ]);
-                        },
-                    },
+                    getFilterByMenuItem(self),
                     {
                         label: 'Line width',
                         subMenu: [
@@ -166,70 +110,51 @@ function stateModelFactory(configSchema) {
                         ],
                     },
                     {
-                        label: 'Draw inter-region vertical lines',
-                        type: 'checkbox',
-                        checked: self.drawInter,
-                        onClick: () => {
-                            self.setDrawInter(!self.drawInter);
-                        },
-                    },
-                    {
-                        label: 'Draw long range connections',
-                        type: 'checkbox',
-                        checked: self.drawLongRange,
-                        onClick: () => {
-                            self.setDrawLongRange(!self.drawLongRange);
-                        },
-                    },
-                    {
-                        label: 'Color scheme',
-                        icon: PaletteIcon,
+                        label: 'Show...',
+                        type: 'subMenu',
                         subMenu: [
                             {
-                                label: 'Insert size ± 3σ and orientation',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'insertSizeAndOrientation' });
-                                },
-                            },
-                            {
-                                label: 'Insert size ± 3σ',
+                                label: 'Show legend',
+                                type: 'checkbox',
+                                checked: self.showLegend,
                                 onClick: () => {
-                                    self.setColorScheme({ type: 'insertSize' });
+                                    self.setShowLegend(!self.showLegend);
                                 },
                             },
                             {
-                                label: 'Orientation',
+                                label: 'Inter-chromosomal connections (purple vertical lines)',
+                                type: 'checkbox',
+                                checked: self.drawInter,
                                 onClick: () => {
-                                    self.setColorScheme({ type: 'orientation' });
+                                    self.setDrawInter(!self.drawInter);
                                 },
                             },
                             {
-                                label: 'Insert size gradient',
+                                label: 'Long range connections (red vertical lines)',
+                                type: 'checkbox',
+                                checked: self.drawLongRange,
                                 onClick: () => {
-                                    self.setColorScheme({ type: 'gradient' });
+                                    self.setDrawLongRange(!self.drawLongRange);
                                 },
                             },
                         ],
                     },
+                    getColorSchemeMenuItem(self),
                 ];
             },
+            async renderSvg(opts) {
+                const { renderSvg } = await import("./renderSvg.js");
+                return renderSvg(self, opts);
+            },
         };
     })
-        .views(self => ({
-        async renderSvg(opts) {
-            const { renderSvg } = await import('../shared/renderSvgUtil');
-            const { drawFeats } = await import('./drawFeats');
-            return renderSvg(self, opts, drawFeats);
-        },
-    }))
         .actions(self => ({
         afterAttach() {
             ;
             (async () => {
                 try {
-                    const { doAfterAttach } = await import('../shared/afterAttach');
-                    const { drawFeats } = await import('./drawFeats');
-                    doAfterAttach(self, drawFeats);
+                    const { doAfterAttachRPC } = await import("./afterAttachRPC.js");
+                    doAfterAttachRPC(self);
                 }
                 catch (e) {
                     console.error(e);
@@ -237,6 +162,20 @@ function stateModelFactory(configSchema) {
                 }
             })();
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { lineWidth, jitter, drawInter, drawLongRange, showLegend, ...rest } = snap;
+        return {
+            ...rest,
+            ...(lineWidth !== undefined ? { lineWidth } : {}),
+            ...(jitter !== undefined ? { jitter } : {}),
+            ...(!drawInter ? { drawInter } : {}),
+            ...(!drawLongRange ? { drawLongRange } : {}),
+            ...(showLegend !== undefined ? { showLegend } : {}),
+        };
+    });
 }
 export default stateModelFactory;

package/esm/LinearReadArcsDisplay/renderSvg.d.ts

@@ -0,0 +1,3 @@
+import type { LinearReadArcsDisplayModel } from './model.ts';
+import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+export declare function renderSvg(self: LinearReadArcsDisplayModel, opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;