@jbrowse/plugin-linear-comparative-view 2.12.0 → 2.12.1

package/dist/LinearComparativeView/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance, SnapshotIn } from 'mobx-state-tree';
 import { MenuItem } from '@jbrowse/core/ui';
 import PluginManager from '@jbrowse/core/PluginManager';
@@ -52,15 +51,15 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         volatileWidth: number | undefined;
         minimumBlockWidth: number;
-        draggingTrackId: string | undefined;
+        draggingTrackId: undefined | string;
         volatileError: unknown;
         afterDisplayedRegionsSetCallbacks: Function[];
         scaleFactor: number;
         trackRefs: Record<string, HTMLDivElement>;
         coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
         coarseTotalBp: number;
-        leftOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
-        rightOffset: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined;
+        leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
+        rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset;
     } & {
         readonly trackLabelsSetting: any;
         readonly width: number;
@@ -109,8 +108,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
-        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
-        setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string | undefined): void;
+        setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
         setNewView(bpPerPx: number, offsetPx: number): void;
         horizontallyFlip(): void;
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
@@ -123,30 +122,30 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
-        setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
+        setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
         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 | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
+        getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): {
             start: number;
             end: number;
             type: string;
-            regionNumber?: number | undefined;
-            reversed?: boolean | undefined;
+            regionNumber?: number;
+            reversed?: boolean;
             refName: string;
             assemblyName: string;
             key: string;
             offsetPx: number;
             widthPx: number;
-            variant?: string | undefined;
-            isLeftEndOfDisplayedRegion?: boolean | undefined;
+            variant?: string;
+            isLeftEndOfDisplayedRegion?: boolean;
         }[];
         afterDisplayedRegionsSet(cb: Function): void;
         horizontalScroll(distance: number): number;
         center(): void;
         showAllRegions(): void;
-        showAllRegionsInAssembly(assemblyName?: string | undefined): void;
-        setDraggingTrackId(idx?: string | undefined): void;
+        showAllRegionsInAssembly(assemblyName?: string): void;
+        setDraggingTrackId(idx?: string): void;
         setScaleFactor(factor: number): void;
         clearView(): void;
         exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions): Promise<void>;
@@ -171,141 +170,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
         afterAttach(): void;
     } & {
-        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
-        navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+        moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset): void;
+        navToLocString(input: string, optAssemblyName?: string): Promise<void>;
         navToSearchString({ input, assembly, }: {
             input: string;
-            assembly: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
-                 * #property
-                 */
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
-                 * #property
-                 */
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
         }): Promise<void>;
-        navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): 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;
     } & {
@@ -313,12 +184,12 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         bpToPx({ refName, coord, regionNumber, }: {
             refName: string;
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number;
         }): {
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
+        centerAt(coord: number, refName: string, regionNumber?: number): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -328,7 +199,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             offset: number;
             start: number;
             end: number;
-            reversed?: boolean | undefined;
+            reversed?: boolean;
         };
         readonly centerLineInfo: {
             coord: number;
@@ -339,7 +210,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             offset: number;
             start: number;
             end: number;
-            reversed?: boolean | undefined;
+            reversed?: boolean;
         } | undefined;
     } & {
         afterCreate(): void;

package/dist/LinearReadVsRef/LinearReadVsRef.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ReadVsRefDialog;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
@@ -281,4 +282,3 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel"),
             react_1.default.createElement(material_1.Button, { disabled: !primaryFeature, variant: "contained", color: "primary", onClick: onSubmit }, "Submit"))));
 }
-exports.default = ReadVsRefDialog;

package/dist/LinearReadVsRef/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearReadVsRefMenuItemF;
 const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
 // icons
@@ -75,4 +76,3 @@ function LinearReadVsRefMenuItemF(pm) {
         return pluggableElement;
     });
 }
-exports.default = LinearReadVsRefMenuItemF;

package/dist/LinearSyntenyDisplay/afterAttach.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.doAfterAttach = void 0;
+exports.doAfterAttach = doAfterAttach;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
@@ -103,4 +103,3 @@ function doAfterAttach(self) {
         self.setFeatPositions(map);
     }, { fireImmediately: true }));
 }
-exports.doAfterAttach = doAfterAttach;

package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SyntenyContextMenu;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
@@ -54,4 +55,3 @@ function SyntenyContextMenu({ model, onClose, anchorEl, }) {
             },
         ] }));
 }
-exports.default = SyntenyContextMenu;

package/dist/LinearSyntenyDisplay/components/util.js

@@ -1,6 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTooltip = exports.onSynContextClick = exports.onSynClick = exports.drawBezierBox = exports.drawBox = exports.draw = exports.drawMatchSimple = void 0;
+exports.drawMatchSimple = drawMatchSimple;
+exports.draw = draw;
+exports.drawBox = drawBox;
+exports.drawBezierBox = drawBezierBox;
+exports.onSynClick = onSynClick;
+exports.onSynContextClick = onSynContextClick;
+exports.getTooltip = getTooltip;
 const util_1 = require("@jbrowse/core/util");
 // locals
 const drawSynteny_1 = require("../drawSynteny");
@@ -42,7 +48,6 @@ function drawMatchSimple({ feature, ctx, offsets, cb, height, drawCurves, oobLim
         cb(ctx);
     }
 }
-exports.drawMatchSimple = drawMatchSimple;
 function draw(ctx, x1, x2, y1, x3, x4, y2, mid, drawCurves) {
     if (drawCurves) {
         drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid);
@@ -51,7 +56,6 @@ function draw(ctx, x1, x2, y1, x3, x4, y2, mid, drawCurves) {
         drawBox(ctx, x1, x2, y1, x3, x4, y2);
     }
 }
-exports.draw = draw;
 function drawBox(ctx, x1, x2, y1, x3, x4, y2) {
     ctx.beginPath();
     ctx.moveTo(x1, y1);
@@ -61,7 +65,6 @@ function drawBox(ctx, x1, x2, y1, x3, x4, y2) {
     ctx.closePath();
     ctx.fill();
 }
-exports.drawBox = drawBox;
 function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     const len1 = Math.abs(x1 - x2);
     const len2 = Math.abs(x1 - x2);
@@ -82,7 +85,6 @@ function drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid) {
     ctx.closePath();
     ctx.fill();
 }
-exports.drawBezierBox = drawBezierBox;
 function onSynClick(event, model) {
     const ref1 = model.clickMapCanvas;
     const ref2 = model.cigarClickMapCanvas;
@@ -116,7 +118,6 @@ function onSynClick(event, model) {
     }
     return feat;
 }
-exports.onSynClick = onSynClick;
 function onSynContextClick(event, model, setAnchorEl) {
     event.preventDefault();
     const ref1 = model.clickMapCanvas;
@@ -142,7 +143,6 @@ function onSynContextClick(event, model, setAnchorEl) {
         setAnchorEl({ clientX, clientY, feature: f });
     }
 }
-exports.onSynContextClick = onSynContextClick;
 function getTooltip(f, cigarOp, cigarOpLen) {
     // @ts-expect-error
     const f1 = f.toJSON();
@@ -166,4 +166,3 @@ function getTooltip(f, cigarOp, cigarOpLen) {
         .filter(f => !!f)
         .join('<br/>');
 }
-exports.getTooltip = getTooltip;

package/dist/LinearSyntenyDisplay/drawSynteny.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawMouseoverSynteny = exports.drawRef = exports.getId = exports.MAX_COLOR_RANGE = void 0;
+exports.MAX_COLOR_RANGE = void 0;
+exports.getId = getId;
+exports.drawRef = drawRef;
+exports.drawMouseoverSynteny = drawMouseoverSynteny;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./components/util");
 exports.MAX_COLOR_RANGE = 255 * 255 * 255; // max color range
@@ -23,7 +26,6 @@ const oobLimit = 1600;
 function getId(r, g, b, unitMultiplier) {
     return Math.floor((r * 255 * 255 + g * 255 + b - 1) / unitMultiplier);
 }
-exports.getId = getId;
 function drawRef(model, ctx1, ctx3) {
     var _a;
     const view = (0, util_1.getContainingView)(model);
@@ -183,7 +185,6 @@ function drawRef(model, ctx1, ctx3) {
         });
     }
 }
-exports.drawRef = drawRef;
 function drawMouseoverSynteny(model) {
     var _a;
     const { clickId, mouseoverId } = model;
@@ -229,4 +230,3 @@ function drawMouseoverSynteny(model) {
         });
     }
 }
-exports.drawMouseoverSynteny = drawMouseoverSynteny;

package/dist/LinearSyntenyDisplay/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearSyntenyDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 // locals
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
@@ -44,4 +45,3 @@ function LinearSyntenyDisplayF(pluginManager) {
         });
     });
 }
-exports.default = LinearSyntenyDisplayF;

package/dist/LinearSyntenyDisplay/model.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
@@ -58,8 +57,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function | undefined;
-        blockState?: Record<string, any> | undefined;
+        onHorizontalScroll?: Function;
+        blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{
         model: {
@@ -82,19 +81,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
-    renderProps(): any; /**
-     * #getter
-     */
+    renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-     * #getter
-     * used for synteny svg rendering
-     */
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string | undefined): void;
+    setMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -112,7 +106,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             configuration: {
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                        [x: string]: any;
+                    } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+                } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
             } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
             height: number;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -138,8 +138,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -162,19 +162,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -213,8 +208,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     error: unknown;
                     message: string | undefined;
                 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-                onHorizontalScroll?: Function | undefined;
-                blockState?: Record<string, any> | undefined;
+                onHorizontalScroll?: Function;
+                blockState?: Record<string, any>;
             }>;
             readonly DisplayBlurb: import("react").FC<{
                 model: {
@@ -237,19 +232,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: any;
-            renderProps(): any; /**
-             * #getter
-             */
+            renderProps(): any;
             readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-            readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+            readonly DisplayMessageComponent: undefined | import("react").FC<any>;
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[]; /**
-             * #getter
-             * used for synteny svg rendering
-             */
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
             regionCannotBeRendered(): null;
         } & {
-            setMessage(arg?: string | undefined): void;
+            setMessage(arg?: string): void;
             setError(error?: unknown): void;
             setRpcDriverName(rpcDriverName: string): void;
             reload(): void;
@@ -265,7 +255,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setMessage(messageText: string): void;
     setRendered(args?: {
         features: Feature[];
-    } | undefined): void;
+    }): void;
     setError(error: unknown): void;
 } & {
     afterAttach(): void;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ExportSvgDialog;
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
@@ -85,4 +86,3 @@ function ExportSvgDialog({ model, handleClose, }) {
                     }
                 } }, "Submit"))));
 }
-exports.default = ExportSvgDialog;

package/dist/LinearSyntenyView/components/Icons.js

@@ -3,16 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StraightLines = exports.Curves = void 0;
+exports.Curves = Curves;
+exports.StraightLines = StraightLines;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 function Curves(props) {
     return (react_1.default.createElement(material_1.SvgIcon, { ...props },
         react_1.default.createElement("path", { fill: "currentColor", d: "M16.5,21C13.5,21 12.31,16.76 11.05,12.28C10.14,9.04 9,5 7.5,5C4.11,5 4,11.93 4,12H2C2,11.63 2.06,3 7.5,3C10.5,3 11.71,7.25 12.97,11.74C13.83,14.8 15,19 16.5,19C19.94,19 20.03,12.07 20.03,12H22.03C22.03,12.37 21.97,21 16.5,21Z" })));
 }
-exports.Curves = Curves;
 function StraightLines(props) {
     return (react_1.default.createElement(material_1.SvgIcon, { ...props },
         react_1.default.createElement("path", { fill: "currentColor", d: "M22 12L17 22L7.1 6.04L4.24 12H2L7 2L16.9 17.96L19.76 12H22Z" })));
 }
-exports.StraightLines = StraightLines;

package/dist/LinearSyntenyView/components/ImportForm/util.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.extName = exports.basename = exports.stripGz = exports.getName = void 0;
+exports.getName = getName;
+exports.stripGz = stripGz;
+exports.basename = basename;
+exports.extName = extName;
 function getName(sessionTrackData) {
     return sessionTrackData
         ? // @ts-expect-error
@@ -11,17 +14,13 @@ function getName(sessionTrackData) {
                 sessionTrackData.name
         : undefined;
 }
-exports.getName = getName;
 function stripGz(fileName) {
     return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
 }
-exports.stripGz = stripGz;
 function basename(str) {
     return str.split('#')[0].split('?')[0].split('/').pop();
 }
-exports.basename = basename;
 function extName(str) {
     const r = str.split('.').pop();
     return r ? `.${r}` : '';
 }
-exports.extName = extName;

package/dist/LinearSyntenyView/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearSyntenyViewF;
 const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
@@ -39,4 +40,3 @@ function LinearSyntenyViewF(pluginManager) {
         });
     });
 }
-exports.default = LinearSyntenyViewF;