@jbrowse/plugin-linear-genome-view 2.10.3 → 2.11.0

package/dist/index.d.ts

@@ -946,7 +946,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
-                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
+                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;
             } & {
@@ -1004,6 +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;
@@ -1011,7 +1013,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -1021,6 +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;
@@ -1214,7 +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;
@@ -1267,7 +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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+                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;
             } & {
@@ -1325,6 +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;
@@ -1332,7 +1342,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -1342,6 +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;
@@ -1535,7 +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;
@@ -1560,7 +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: {
@@ -1598,7 +1644,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
-                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
+                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;
             } & {
@@ -1656,6 +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;
@@ -1663,7 +1711,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -1673,6 +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;
@@ -1866,7 +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;
@@ -1919,7 +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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+                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;
             } & {
@@ -1977,6 +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;
@@ -1984,7 +2040,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -1994,6 +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;
@@ -2187,7 +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;
@@ -2212,7 +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: {
@@ -2250,7 +2342,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
-                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
+                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;
             } & {
@@ -2308,6 +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;
@@ -2315,7 +2409,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -2325,6 +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;
@@ -2518,7 +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;
@@ -2571,7 +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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+                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;
             } & {
@@ -2629,6 +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;
@@ -2636,7 +2738,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
-                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): 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;
@@ -2646,6 +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;
@@ -2839,7 +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;
@@ -2864,7 +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/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -96,7 +96,6 @@ const blockState = types
             renderInProgress = undefined;
         },
         setError(error) {
-            console.error(error);
             if (renderInProgress && !renderInProgress.signal.aborted) {
                 renderInProgress.abort();
             }

package/esm/LaunchLinearGenomeView/index.js

@@ -23,11 +23,19 @@ export default (pluginManager) => {
                 view.setHideHeader(!nav);
             }
             if (highlight !== undefined) {
-                const location = parseLocString(highlight, refName => isValidRefName(refName, assembly));
-                if ((location === null || location === void 0 ? void 0 : location.start) !== undefined && (location === null || location === void 0 ? void 0 : location.end) !== undefined) {
-                    location.assemblyName = assembly;
-                    view.setHighlight(location);
-                }
+                highlight.forEach(async (h) => {
+                    if (h) {
+                        const parsedLocString = parseLocString(h, refName => isValidRefName(refName, assembly));
+                        const location = {
+                            ...parsedLocString,
+                            assemblyName: assembly,
+                        };
+                        if ((location === null || location === void 0 ? void 0 : location.start) !== undefined &&
+                            (location === null || location === void 0 ? void 0 : location.end) !== undefined) {
+                            view.addToHighlights(location);
+                        }
+                    }
+                });
             }
             await handleSelectedRegion({ input: loc, model: view, assembly: asm });
             const idsNotFound = [];
@@ -37,7 +45,7 @@ export default (pluginManager) => {
             }
         }
         catch (e) {
-            session.notify(`${e}`, 'error');
+            session.notifyError(`${e}`, e);
             throw e;
         }
     });

package/esm/LinearBasicDisplay/components/SetMaxHeight.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 declare const SetMaxHeightDialog: ({ model, handleClose, }: {
     model: {
-        maxHeight?: number | undefined;
+        maxHeight?: number;
         setMaxHeight: (arg?: number) => void;
     };
     handleClose: () => void;

package/esm/LinearGenomeView/components/Cytobands.d.ts

@@ -4,131 +4,7 @@ import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 declare const Cytobands: ({ overview, block, assembly, }: {
     overview: Base1DViewModel;
-    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;
-    } & {
-        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;
-    } & {
-        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>>) | undefined;
+    assembly?: Assembly;
     block: ContentBlock;
 }) => React.JSX.Element;
 export default Cytobands;