npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.10.2 → 2.11.0 - Mend

@jbrowse/plugin-linear-genome-view 2.10.2 → 2.11.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (75) hide show

package/esm/index.d.ts CHANGED Viewed

@@ -38,8 +38,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -83,8 +90,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -292,8 +306,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -497,8 +518,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     message: string | undefined;
                     maxHeightReached: boolean;
                     ReactComponent: ({ model, }: {
-                        model: any;
-                    }) => any;
+                        model: {
+                            error?: unknown;
+                            reload: () => void;
+                            message: import("react").ReactNode;
+                            filled?: boolean | undefined;
+                            status?: string | undefined;
+                            reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                        };
+                    }) => import("react").JSX.Element | undefined;
                     renderProps: any;
                 } & {
                     doReload(): void;
@@ -587,8 +615,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string | undefined;
                 maxHeightReached: boolean;
                 ReactComponent: ({ model, }: {
-                    model: any;
-                }) => any;
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message: import("react").ReactNode;
+                        filled?: boolean | undefined;
+                        status?: string | undefined;
+                        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    };
+                }) => import("react").JSX.Element | undefined;
                 renderProps: any;
             } & {
                 doReload(): void;
@@ -792,8 +827,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 message: string | undefined;
                 maxHeightReached: boolean;
                 ReactComponent: ({ model, }: {
-                    model: any;
-                }) => any;
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message: import("react").ReactNode;
+                        filled?: boolean | undefined;
+                        status?: string | undefined;
+                        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                    };
+                }) => import("react").JSX.Element | undefined;
                 renderProps: any;
             } & {
                 doReload(): void;
@@ -904,6 +946,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
+                colorByCDS: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -961,6 +1005,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -968,6 +1013,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -977,6 +1025,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -1170,7 +1222,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -1223,6 +1275,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }, {
                 width: number;
             } & {
@@ -1280,6 +1334,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -1287,6 +1342,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1296,6 +1354,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -1489,7 +1551,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -1514,7 +1576,37 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 } | undefined;
             } & {
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+                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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            } & {
+                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
+                offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+                    refName: import("mobx-state-tree").ISimpleType<string>;
+                    start: import("mobx-state-tree").ISimpleType<number>;
+                    end: import("mobx-state-tree").ISimpleType<number>;
+                    reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                } & {
+                    assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                }, {
+                    setRefName(newRefName: string): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+                hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            }>>, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
         ZoomControls: ({ model, }: {
             model: {
@@ -1552,6 +1644,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
+                colorByCDS: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -1609,6 +1703,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -1616,6 +1711,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1625,6 +1723,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -1818,7 +1920,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -1871,6 +1973,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }, {
                 width: number;
             } & {
@@ -1928,6 +2032,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -1935,6 +2040,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1944,6 +2052,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -2137,7 +2249,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -2162,7 +2274,37 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 } | undefined;
             } & {
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+                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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            } & {
+                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
+                offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+                    refName: import("mobx-state-tree").ISimpleType<string>;
+                    start: import("mobx-state-tree").ISimpleType<number>;
+                    end: import("mobx-state-tree").ISimpleType<number>;
+                    reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                } & {
+                    assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                }, {
+                    setRefName(newRefName: string): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+                hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            }>>, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
         LinearGenomeView: ({ model }: {
             model: {
@@ -2200,6 +2342,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
+                colorByCDS: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -2257,6 +2401,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -2264,6 +2409,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2273,6 +2421,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -2466,7 +2618,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -2519,6 +2671,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
             }, {
                 width: number;
             } & {
@@ -2576,6 +2730,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
                 readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
             } & {
+                setColorByCDS(flag: boolean): void;
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
@@ -2583,6 +2738,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+                removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2592,6 +2750,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
                 hideTrack(trackId: string): number;
             } & {
+                moveTrackDown(id: string): void;
+                moveTrackUp(id: string): void;
+                moveTrackToTop(id: string): void;
+                moveTrackToBottom(id: string): void;
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
@@ -2785,7 +2947,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     index: number;
                     offsetPx: number;
                 } | undefined;
-                centerAt(coord: number, refName: string, regionNumber: number): void;
+                centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
                 pxToBp(px: number): {
                     coord: number;
                     index: number;
@@ -2810,7 +2972,37 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 } | undefined;
             } & {
                 afterCreate(): void;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+                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>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            } & {
+                id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
+                offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+                displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+                    refName: import("mobx-state-tree").ISimpleType<string>;
+                    start: import("mobx-state-tree").ISimpleType<number>;
+                    end: import("mobx-state-tree").ISimpleType<number>;
+                    reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                } & {
+                    assemblyName: import("mobx-state-tree").ISimpleType<string>;
+                }, {
+                    setRefName(newRefName: string): void;
+                }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+                tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+                hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+                showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                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<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+                colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            }>>, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
     };
     /**

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.10.2",
+  "version": "2.11.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }