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

package/dist/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/dist/LinearSyntenyView/model.js

@@ -15,69 +15,66 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelFactory;
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const util_1 = require("@jbrowse/core/util");
-const file_saver_1 = require("file-saver");
-// icons
 const CropFree_1 = __importDefault(require("@mui/icons-material/CropFree"));
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const Link_1 = __importDefault(require("@mui/icons-material/Link"));
 const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const file_saver_1 = require("file-saver");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const Icons_1 = require("./components/Icons");
-// locals
 const model_1 = __importDefault(require("../LinearComparativeView/model"));
-// lazies
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
-/**
- * #stateModel LinearSyntenyView
- * extends
- * - [LinearComparativeView](../linearcomparativeview)
- */
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .compose('LinearSyntenyView', (0, model_1.default)(pluginManager), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearSyntenyView'),
-        /**
-         * #property/
-         */
         drawCIGAR: true,
-        /**
-         * #property
-         */
         drawCurves: false,
+    }))
+        .volatile(() => ({
+        importFormSyntenyTrackSelections: mobx_1.observable.array(),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
-        toggleCurves() {
-            self.drawCurves = !self.drawCurves;
+        importFormRemoveRow(idx) {
+            self.importFormSyntenyTrackSelections.splice(idx, 1);
+        },
+        clearImportFormSyntenyTracks() {
+            self.importFormSyntenyTrackSelections.clear();
         },
-        /**
-         * #action
-         */
-        toggleCIGAR() {
-            self.drawCIGAR = !self.drawCIGAR;
+        setImportFormSyntenyTrack(arg, val) {
+            self.importFormSyntenyTrackSelections[arg] = val;
+        },
+        setDrawCurves(arg) {
+            self.drawCurves = arg;
+        },
+        setDrawCIGAR(arg) {
+            self.drawCIGAR = arg;
         },
-        /**
-         * #action
-         */
         showAllRegions() {
             (0, mobx_1.transaction)(() => {
                 for (const view of self.views) {
@@ -87,9 +84,6 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async exportSvg(opts) {
             const { renderToSvg } = await Promise.resolve().then(() => __importStar(require('./svgcomponents/SVGLinearSyntenyView')));
             const html = await renderToSvg(self, opts);
@@ -101,11 +95,6 @@ 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(),
@@ -123,17 +112,30 @@ 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: Link_1.default,
+                        onClick: () => {
+                            self.setLinkViews(!self.linkViews);
+                        },
+                    },
                     {
                         label: 'Use curved lines',
                         type: 'checkbox',
                         checked: self.drawCurves,
-                        onClick: self.toggleCurves,
                         icon: Icons_1.Curves,
+                        onClick: () => {
+                            self.setDrawCurves(!self.drawCurves);
+                        },
                     },
                     {
                         label: 'Export SVG',
@@ -141,15 +143,15 @@ function stateModelFactory(pluginManager) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 ExportSvgDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
                 ];
             },
-            /**
-             * #method
-             */
             menuItems() {
                 return [
                     ...superMenuItems(),
@@ -159,7 +161,10 @@ function stateModelFactory(pluginManager) {
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 ExportSvgDialog,
-                                { model: self, handleClose },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/dist/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/dist/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -1,13 +1,10 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGBackground;
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
+    return ((0, jsx_runtime_1.jsx)("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }

package/dist/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/dist/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js

@@ -1,19 +1,11 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SVGLinearGenomeView;
-const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const material_1 = require("@mui/material");
 function SVGLinearGenomeView({ trackLabelOffset, fontSize, textHeight, trackLabels, view, displayResults, rulerHeight, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },
-        react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
-            react_1.default.createElement("text", { x: 0, fontSize: fontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, view.assemblyNames.join(', ')),
-            react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults.view, fontSize: fontSize })),
-        react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + fontSize})` },
-            react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }))));
+    return ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} ${fontSize})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 0, fontSize: fontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary), children: view.assemblyNames.join(', ') }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGRuler, { model: displayResults.view, fontSize: fontSize })] }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${rulerHeight + fontSize})`, children: (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults.view, displayResults: displayResults.data, trackLabelOffset: trackLabelOffset }) })] }));
 }

package/dist/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>;