@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/esm/LinearSyntenyView/model.d.ts

@@ -1,7 +1,8 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type React from 'react';
 import { Curves } from './components/Icons';
+import type { ImportFormSyntenyTrack } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     scale?: number;
@@ -18,11 +19,6 @@ export interface ExportSvgOptions {
     themeName?: string;
     trackLabels?: string;
 }
-/**
- * #stateModel LinearSyntenyView
- * extends
- * - [LinearComparativeView](../linearcomparativeview)
- */
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -32,7 +28,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -66,7 +63,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -87,8 +84,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -98,6 +95,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -134,12 +132,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -156,7 +154,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -178,7 +176,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -200,15 +198,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -263,7 +261,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;
@@ -287,12 +285,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     readonly refNames: string[][];
     readonly assemblyNames: string[];
 } & {
+    afterAttach(): void;
     beforeDestroy(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
     setWidth(newWidth: number): void;
     setViews(views: import("mobx-state-tree").SnapshotIn<import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel>[]): void;
     removeView(view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewModel): void;
     setLevelHeight(newHeight: number, level?: number): number;
+    setLinkViews(arg: boolean): void;
     activateTrackSelector(level: number): import("@jbrowse/core/util").Widget;
     toggleTrack(trackId: string, level?: number): void;
     showTrack(trackId: string, level?: number, initialSnapshot?: {}): void;
@@ -310,29 +310,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     afterAttach(): void;
 } & {
-    /**
-     * #action
-     */
-    toggleCurves(): void;
-    /**
-     * #action
-     */
-    toggleCIGAR(): void;
-    /**
-     * #action
-     */
+    importFormSyntenyTrackSelections: import("mobx").IObservableArray<ImportFormSyntenyTrack>;
+} & {
+    importFormRemoveRow(idx: number): void;
+    clearImportFormSyntenyTracks(): void;
+    setImportFormSyntenyTrack(arg: number, val: ImportFormSyntenyTrack): void;
+    setDrawCurves(arg: boolean): void;
+    setDrawCIGAR(arg: boolean): void;
     showAllRegions(): void;
 } & {
-    /**
-     * #action
-     */
     exportSvg(opts: ExportSvgOptions): Promise<void>;
 } & {
-    /**
-     * #method
-     * includes a subset of view menu options because the full list is a
-     * little overwhelming
-     */
     headerMenuItems(): (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;
         onClick: () => void;
@@ -353,8 +341,17 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         label: string;
         type: string;
         checked: boolean;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         onClick: () => void;
+        description?: undefined;
+    } | {
+        label: string;
+        type: string;
+        checked: boolean;
         icon: typeof Curves;
+        onClick: () => void;
         description?: undefined;
     } | {
         label: string;
@@ -366,9 +363,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         checked?: undefined;
         type?: undefined;
     })[];
-    /**
-     * #method
-     */
     menuItems(): (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">> & {
@@ -387,7 +381,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    interactiveOverlay: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     levels: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -421,7 +416,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
@@ -442,8 +437,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
-        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -453,6 +448,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         scaleBarDisplayPrefix(): string | undefined;
         MiniControlsComponent(): React.FC<any>;
         HeaderComponent(): React.FC<any>;
+        readonly assembliesNotFound: string | undefined;
         readonly assemblyErrors: string;
         readonly assembliesInitialized: boolean;
         readonly initialized: boolean;
@@ -489,12 +485,12 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
-        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType[]): void;
-        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType): void;
+        addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
+        setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
+        removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
@@ -511,7 +507,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setShowCenterLine(b: boolean): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
         activateTrackSelector(): import("@jbrowse/core/util").Widget;
-        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
             start: number;
             end: number;
             type: string;
@@ -533,7 +529,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
-        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
     } & {
         slide: (viewWidths: number) => void;
     } & {
@@ -555,15 +551,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
         navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
             assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
-        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
-        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
+        navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
+        navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
     } & {
         rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
         bpToPx({ refName, coord, regionNumber, }: {
@@ -618,7 +614,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").HighlightType>>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
         colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>, import("mobx-state-tree")._NotCustomized>>;

package/esm/LinearSyntenyView/model.js

@@ -1,54 +1,41 @@
 import { lazy } from 'react';
-import { types } from 'mobx-state-tree';
-import { transaction } from 'mobx';
 import { getSession } from '@jbrowse/core/util';
-import { saveAs } from 'file-saver';
-// icons
 import CropFreeIcon from '@mui/icons-material/CropFree';
-import VisibilityIcon from '@mui/icons-material/Visibility';
+import LinkIcon from '@mui/icons-material/Link';
 import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
+import VisibilityIcon from '@mui/icons-material/Visibility';
+import { saveAs } from 'file-saver';
+import { observable, transaction } from 'mobx';
+import { types } from 'mobx-state-tree';
 import { Curves } from './components/Icons';
-// locals
 import baseModel from '../LinearComparativeView/model';
-// lazies
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
-/**
- * #stateModel LinearSyntenyView
- * extends
- * - [LinearComparativeView](../linearcomparativeview)
- */
 export default function stateModelFactory(pluginManager) {
     return types
         .compose('LinearSyntenyView', baseModel(pluginManager), types.model({
-        /**
-         * #property
-         */
         type: types.literal('LinearSyntenyView'),
-        /**
-         * #property/
-         */
         drawCIGAR: true,
-        /**
-         * #property
-         */
         drawCurves: false,
+    }))
+        .volatile(() => ({
+        importFormSyntenyTrackSelections: observable.array(),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
-        toggleCurves() {
-            self.drawCurves = !self.drawCurves;
+        importFormRemoveRow(idx) {
+            self.importFormSyntenyTrackSelections.splice(idx, 1);
+        },
+        clearImportFormSyntenyTracks() {
+            self.importFormSyntenyTrackSelections.clear();
+        },
+        setImportFormSyntenyTrack(arg, val) {
+            self.importFormSyntenyTrackSelections[arg] = val;
+        },
+        setDrawCurves(arg) {
+            self.drawCurves = arg;
         },
-        /**
-         * #action
-         */
-        toggleCIGAR() {
-            self.drawCIGAR = !self.drawCIGAR;
+        setDrawCIGAR(arg) {
+            self.drawCIGAR = arg;
         },
-        /**
-         * #action
-         */
         showAllRegions() {
             transaction(() => {
                 for (const view of self.views) {
@@ -58,9 +45,6 @@ export default function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async exportSvg(opts) {
             const { renderToSvg } = await import('./svgcomponents/SVGLinearSyntenyView');
             const html = await renderToSvg(self, opts);
@@ -72,11 +56,6 @@ export default function stateModelFactory(pluginManager) {
         const superHeaderMenuItems = self.headerMenuItems;
         const superMenuItems = self.menuItems;
         return {
-            /**
-             * #method
-             * includes a subset of view menu options because the full list is a
-             * little overwhelming
-             */
             headerMenuItems() {
                 return [
                     ...superHeaderMenuItems(),
@@ -94,17 +73,30 @@ export default function stateModelFactory(pluginManager) {
                     },
                     {
                         label: 'Draw CIGAR',
-                        onClick: self.toggleCIGAR,
+                        onClick: () => {
+                            self.setDrawCIGAR(!self.drawCIGAR);
+                        },
                         checked: self.drawCIGAR,
                         type: 'checkbox',
                         description: 'Draws per-base CIGAR level alignments',
                     },
+                    {
+                        label: 'Link views',
+                        type: 'checkbox',
+                        checked: self.linkViews,
+                        icon: LinkIcon,
+                        onClick: () => {
+                            self.setLinkViews(!self.linkViews);
+                        },
+                    },
                     {
                         label: 'Use curved lines',
                         type: 'checkbox',
                         checked: self.drawCurves,
-                        onClick: self.toggleCurves,
                         icon: Curves,
+                        onClick: () => {
+                            self.setDrawCurves(!self.drawCurves);
+                        },
                     },
                     {
                         label: 'Export SVG',
@@ -112,15 +104,15 @@ export default function stateModelFactory(pluginManager) {
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 ExportSvgDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
                 ];
             },
-            /**
-             * #method
-             */
             menuItems() {
                 return [
                     ...superMenuItems(),
@@ -130,7 +122,10 @@ export default function stateModelFactory(pluginManager) {
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 ExportSvgDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 export default function SVGBackground({ width, height, shift, }: {
     width: number;
     height: number;
     shift: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -1,7 +1,7 @@
-import React from 'react';
-import { useTheme } from '@mui/material';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { stripAlpha } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
+    return (_jsx("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }: {
     textHeight: number;
     trackLabels: string;
@@ -9,4 +8,4 @@ export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHe
     displayResults: any;
     rulerHeight: number;
     shift: number;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js

@@ -1,13 +1,8 @@
-import React from 'react';
-import { useTheme } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getFillProps } from '@jbrowse/core/util';
-import { SVGTracks, SVGRuler, } from '@jbrowse/plugin-linear-genome-view';
+import { SVGRuler, SVGTracks } from '@jbrowse/plugin-linear-genome-view';
+import { useTheme } from '@mui/material';
 export default function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }) {
     const theme = useTheme();
-    return (React.createElement("g", { transform: `translate(${shift} ${fontSize})` },
-        React.createElement("g", { transform: `translate(${trackLabelOffset})` },
-            React.createElement("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary) }, view.assemblyNames.join(', ')),
-            React.createElement(SVGRuler, { model: displayResults.view, fontSize: fontSize })),
-        React.createElement("g", { transform: `translate(0 ${rulerHeight + fontSize})` },
-            React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }))));
+    return (_jsxs("g", { transform: `translate(${shift} ${fontSize})`, children: [_jsxs("g", { transform: `translate(${trackLabelOffset})`, children: [_jsx("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary), children: view.assemblyNames.join(', ') }), _jsx(SVGRuler, { model: displayResults.view, fontSize: fontSize })] }), _jsx("g", { transform: `translate(0 ${rulerHeight + fontSize})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }) })] }));
 }

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts

@@ -1,2 +1,2 @@
-import { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
+import type { ExportSvgOptions, LinearSyntenyViewModel } from '../model';
 export declare function renderToSvg(model: LinearSyntenyViewModel, opts: ExportSvgOptions): Promise<string>;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -1,16 +1,13 @@
-import React from 'react';
-import { ThemeProvider } from '@mui/material';
-import { getRoot } from 'mobx-state-tree';
-import { when } from 'mobx';
-import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, } from '@jbrowse/core/util';
-import { getTrackName } from '@jbrowse/core/util/tracks';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { ReactRendering, getSerializedSvg, getSession, max, measureText, renderToAbstractCanvas, renderToStaticMarkup, sum, } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
 import { totalHeight } from '@jbrowse/plugin-linear-genome-view';
-// locals
+import { ThemeProvider } from '@mui/material';
+import { when } from 'mobx';
 import SVGBackground from './SVGBackground';
 import SVGLinearGenomeView from './SVGLinearGenomeView';
 import { drawRef } from '../../LinearSyntenyDisplay/drawSynteny';
-// render LGV to SVG
 export async function renderToSvg(model, opts) {
     var _a;
     await when(() => model.initialized);
@@ -20,7 +17,6 @@ export async function renderToSvg(model, opts) {
     const { width, views, levels } = model;
     const shift = 50;
     const offset = rulerHeight;
-    const { createRootFn } = getRoot(model);
     const heights = views.map(v => totalHeight(v.tracks, textHeight, trackLabels) + offset);
     const totalHeightSvg = sum(heights) + sum(levels.map(l => l.height)) + 100;
     const displayResults = await Promise.all(views.map(async (view) => ({
@@ -62,7 +58,7 @@ export async function renderToSvg(model, opts) {
     const w = width + trackLabelOffset;
     const theme = createJBrowseTheme(themeVar);
     const RenderList = [
-        React.createElement(SVGLinearGenomeView, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], key: views[0].id, view: views[0], fontSize: fontSize }),
+        _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, trackLabelOffset: trackLabelOffset, shift: shift, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[0], view: views[0], fontSize: fontSize }, views[0].id),
     ];
     let currOffset = heights[0] + fontSize + rulerHeight;
     for (let i = 1; i < views.length; i++) {
@@ -71,21 +67,8 @@ export async function renderToSvg(model, opts) {
         const rendering = renderings[i - 1];
         const height = heights[i];
         const levelHeight = level.height || 0;
-        RenderList.push(React.createElement("g", { key: view.id, transform: `translate(0 ${currOffset})` },
-            levelHeight ? (React.createElement("defs", null,
-                React.createElement("clipPath", { id: `synclip-${i}` },
-                    React.createElement("rect", { x: 0, y: 0, width: width, height: levelHeight })))) : null,
-            React.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})` }, rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            React.createElement(ReactRendering, { key: i, rendering: r })))),
-            React.createElement("g", { transform: `translate(0 ${levelHeight})` },
-                React.createElement(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], key: view.id, view: view, fontSize: fontSize }))));
+        RenderList.push(_jsxs("g", { transform: `translate(0 ${currOffset})`, children: [levelHeight ? (_jsx("defs", { children: _jsx("clipPath", { id: `synclip-${i}`, children: _jsx("rect", { x: 0, y: 0, width: width, height: levelHeight }) }) })) : null, _jsx("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize})`, clipPath: `url(#synclip-${i})`, children: rendering === null || rendering === void 0 ? void 0 : rendering.map((r, i) => (_jsx(ReactRendering, { rendering: r }, i))) }), _jsx("g", { transform: `translate(0 ${levelHeight})`, children: _jsx(SVGLinearGenomeView, { rulerHeight: rulerHeight, shift: shift, trackLabelOffset: trackLabelOffset, textHeight: textHeight, trackLabels: trackLabels, displayResults: displayResults[i], view: view, fontSize: fontSize }, view.id) })] }, view.id));
         currOffset += height + fontSize + rulerHeight + levelHeight;
     }
-    // the xlink namespace is used for rendering <image> tag
-    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: theme },
-        React.createElement(Wrapper, null,
-            React.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
-                React.createElement(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }),
-                RenderList))), createRootFn);
+    return renderToStaticMarkup(_jsx(ThemeProvider, { theme: theme, children: _jsx(Wrapper, { children: _jsxs("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [_jsx(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }), RenderList] }) }) }));
 }

package/esm/LinearSyntenyView/types.d.ts

@@ -0,0 +1,12 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { SnapshotIn } from 'mobx-state-tree';
+export type Conf = SnapshotIn<AnyConfigurationModel>;
+export type ImportFormSyntenyTrack = {
+    type: 'preConfigured';
+    value: string;
+} | {
+    type: 'userOpened';
+    value: Conf;
+} | {
+    type: 'none';
+};

package/esm/LinearSyntenyView/types.js

@@ -0,0 +1 @@
+export {};

package/esm/LinearSyntenyViewHelper/index.d.ts

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

package/esm/LinearSyntenyViewHelper/index.js

@@ -1,8 +1,8 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
 import { linearSyntenyViewHelperModelFactory } from './stateModelFactory';
 function UnusedComponent() {
-    return React.createElement("div", null);
+    return _jsx("div", {});
 }
 export default function LinearSyntenyViewF(pluginManager) {
     pluginManager.addViewType(() => {