jbrowse-plugin-protein3d 0.0.3 → 0.0.4

package/dist/ProteinView/model.d.ts

@@ -1,10 +1,6 @@
-import { Region as IRegion } from '@jbrowse/core/util/types';
 import { Instance } from 'mobx-state-tree';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { parsePairwise } from 'clustal-js';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
-type MaybeLGV = LGV | undefined;
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import Structure from './structureModel';
 /**
  * #stateModel Protein3dViewPlugin
  * extends
@@ -17,58 +13,496 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"ProteinView">;
-    url: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    data: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    clickGenomeHighlights: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        refName: import(
-        /**
-         * #property
-         * url to structure file
-         */
-        "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>;
+    structures: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        url: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        data: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        pairwiseAlignment: import("mobx-state-tree").IType<import("../mappings").PairwiseAlignment | undefined, import("../mappings").PairwiseAlignment | undefined, import("../mappings").PairwiseAlignment | undefined>;
+        feature: import("mobx-state-tree").IType<import("@jbrowse/core/util").SimpleFeatureSerialized | undefined, import("@jbrowse/core/util").SimpleFeatureSerialized | undefined, import("@jbrowse/core/util").SimpleFeatureSerialized | undefined>;
+        userProvidedTranscriptSequence: import("mobx-state-tree").ISimpleType<string>;
     }, {
-        setRefName(newRefName: string): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    hoverGenomeHighlights: 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]>;
+        model: import("molstar/lib/mol-state").StateObjectSelector<import("molstar/lib/mol-plugin-state/objects").PluginStateObject.Molecule.Model, import("molstar/lib/mol-state").StateTransformer<import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, any>> | undefined;
+        clickGenomeHighlights: import("@jbrowse/core/util").Region[];
+        hoverGenomeHighlights: import("@jbrowse/core/util").Region[];
+        clickPosition: {
+            structureSeqPos: number;
+            code: string;
+            chain: string;
+        } | undefined;
+        hoverPosition: {
+            structureSeqPos?: number;
+            code?: string;
+            chain?: string;
+        } | undefined;
+        pairwiseAlignmentStatus: string;
+        structureSequences: string[] | undefined;
     } & {
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {
-        setRefName(newRefName: string): void;
+        setModel(model: import("molstar/lib/mol-state").StateObjectSelector<import("molstar/lib/mol-plugin-state/objects").PluginStateObject.Molecule.Model, import("molstar/lib/mol-state").StateTransformer<import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, any>>): void;
+        setSequences(str?: string[]): void;
+    } & {
+        readonly connectedView: ({
+            id: string;
+            displayName: string | undefined;
+            minimized: boolean;
+            type: string;
+            offsetPx: number;
+            bpPerPx: number;
+            displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
+            tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
+            hideHeader: boolean;
+            hideHeaderOverview: boolean;
+            hideNoTracksActive: boolean;
+            trackSelectorType: string;
+            showCenterLine: boolean;
+            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;
+            showTrackOutlines: boolean;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            width: number;
+        } & {
+            menuItems(): import("@jbrowse/core/ui").MenuItem[];
+        } & {
+            setDisplayName(name: string): void;
+            setWidth(newWidth: number): void;
+            setMinimized(flag: boolean): void;
+        } & {
+            volatileWidth: number | undefined;
+            minimumBlockWidth: number;
+            draggingTrackId: undefined | string;
+            volatileError: unknown;
+            afterDisplayedRegionsSetCallbacks: Function[];
+            scaleFactor: number;
+            trackRefs: Record<string, HTMLDivElement>;
+            coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+            coarseTotalBp: number;
+            leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset;
+            rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset;
+        } & {
+            readonly trackLabelsSetting: any;
+            readonly width: number;
+            readonly interRegionPaddingWidth: number;
+            readonly assemblyNames: string[];
+        } & {
+            scaleBarDisplayPrefix(): string;
+            MiniControlsComponent(): import("react").FC<any>;
+            HeaderComponent(): import("react").FC<any>;
+            readonly assemblyErrors: string;
+            readonly assembliesInitialized: boolean;
+            readonly initialized: boolean;
+            readonly hasDisplayedRegions: boolean;
+            readonly scaleBarHeight: number;
+            readonly headerHeight: number;
+            readonly trackHeights: number;
+            readonly trackHeightsWithResizeHandles: number;
+            readonly height: number;
+            readonly totalBp: number;
+            readonly maxBpPerPx: number;
+            readonly minBpPerPx: number;
+            readonly error: {};
+            readonly maxOffset: number;
+            readonly minOffset: number;
+            readonly displayedRegionsTotalPx: number;
+            renderProps(): any;
+            searchScope(assemblyName: string): {
+                assemblyName: string;
+                includeAggregateIndexes: boolean;
+                tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
+            };
+            getTrack(id: string): any;
+            rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
+            rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
+            readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
+        } & {
+            setShowTrackOutlines(arg: boolean): void;
+            setColorByCDS(flag: boolean): void;
+            setShowCytobands(flag: boolean): void;
+            setWidth(newWidth: number): void;
+            setError(error: unknown): void;
+            setHideHeader(b: boolean): void;
+            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("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/dist/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;
+            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;
+            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/dist/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset): {
+                start: number;
+                end: number;
+                type: string;
+                regionNumber?: number;
+                reversed?: boolean;
+                refName: string;
+                assemblyName: string;
+                key: string;
+                offsetPx: number;
+                widthPx: number;
+                variant?: string;
+                isLeftEndOfDisplayedRegion?: boolean;
+            }[];
+            afterDisplayedRegionsSet(cb: Function): void;
+            horizontalScroll(distance: number): number;
+            center(): void;
+            showAllRegions(): void;
+            showAllRegionsInAssembly(assemblyName?: string): void;
+            setDraggingTrackId(idx?: string): void;
+            setScaleFactor(factor: number): void;
+            clearView(): void;
+            exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        } & {
+            slide: (viewWidths: number) => void;
+        } & {
+            zoom: (targetBpPerPx: number) => void;
+        } & {
+            readonly canShowCytobands: boolean;
+            readonly showCytobands: boolean;
+            readonly anyCytobandsExist: boolean;
+            readonly cytobandOffset: number;
+        } & {
+            menuItems(): import("@jbrowse/core/ui").MenuItem[];
+        } & {
+            readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+            readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+            readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+            readonly visibleLocStrings: string;
+            readonly coarseVisibleLocStrings: string;
+        } & {
+            setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
+            afterAttach(): void;
+        } & {
+            moveTo(start?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset): void;
+            navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+            navToSearchString({ input, assembly, }: {
+                input: string;
+                assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
+            }): Promise<void>;
+            navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
+            navTo(query: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").NavLocation): void;
+            navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").NavLocation[]): void;
+        } & {
+            rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            bpToPx({ refName, coord, regionNumber, }: {
+                refName: string;
+                coord: number;
+                regionNumber?: number;
+            }): {
+                index: number;
+                offsetPx: number;
+            } | undefined;
+            centerAt(coord: number, refName: string, regionNumber?: number): void;
+            pxToBp(px: number): {
+                coord: number;
+                index: number;
+                refName: string;
+                oob: boolean;
+                assemblyName: string;
+                offset: number;
+                start: number;
+                end: number;
+                reversed?: boolean;
+            };
+            readonly centerLineInfo: {
+                coord: number;
+                index: number;
+                refName: string;
+                oob: boolean;
+                assemblyName: string;
+                offset: number;
+                start: number;
+                end: number;
+                reversed?: boolean;
+            } | undefined;
+        } & {
+            afterCreate(): void;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+            minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        } & {
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
+             * #action
+             */).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" /**
+             * #action
+             */).IType<number | undefined, number, number>;
+            displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+            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]>;
+            showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        }, {
+            width: number;
+        } & {
+            menuItems(): import("@jbrowse/core/ui").MenuItem[];
+        } & {
+            setDisplayName(name: string): void;
+            setWidth(newWidth: number): void;
+            setMinimized(flag: boolean): void;
+        } & {
+            volatileWidth: number | undefined;
+            minimumBlockWidth: number;
+            draggingTrackId: undefined | string;
+            volatileError: unknown;
+            afterDisplayedRegionsSetCallbacks: Function[];
+            scaleFactor: number;
+            trackRefs: Record<string, HTMLDivElement>;
+            coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+            coarseTotalBp: number;
+            leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset;
+            rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset;
+        } & {
+            readonly trackLabelsSetting: any;
+            readonly width: number;
+            readonly interRegionPaddingWidth: number;
+            readonly assemblyNames: string[];
+        } & {
+            scaleBarDisplayPrefix(): string;
+            MiniControlsComponent(): import("react").FC<any>;
+            HeaderComponent(): import("react").FC<any>;
+            readonly assemblyErrors: string;
+            readonly assembliesInitialized: boolean;
+            readonly initialized: boolean;
+            readonly hasDisplayedRegions: boolean;
+            readonly scaleBarHeight: number;
+            readonly headerHeight: number;
+            readonly trackHeights: number;
+            readonly trackHeightsWithResizeHandles: number;
+            readonly height: number;
+            readonly totalBp: number;
+            readonly maxBpPerPx: number;
+            readonly minBpPerPx: number;
+            readonly error: {};
+            readonly maxOffset: number;
+            readonly minOffset: number;
+            readonly displayedRegionsTotalPx: number;
+            renderProps(): any;
+            searchScope(assemblyName: string): {
+                assemblyName: string;
+                includeAggregateIndexes: boolean;
+                tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
+            };
+            getTrack(id: string): any;
+            rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
+            rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
+            readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
+        } & {
+            setShowTrackOutlines(arg: boolean): void;
+            setColorByCDS(flag: boolean): void;
+            setShowCytobands(flag: boolean): void;
+            setWidth(newWidth: number): void;
+            setError(error: unknown): void;
+            setHideHeader(b: boolean): void;
+            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("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/dist/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;
+            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;
+            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/dist/LinearGenomeView").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset): {
+                start: number;
+                end: number;
+                type: string;
+                regionNumber?: number;
+                reversed?: boolean;
+                refName: string;
+                assemblyName: string;
+                key: string;
+                offsetPx: number;
+                widthPx: number;
+                variant?: string;
+                isLeftEndOfDisplayedRegion?: boolean;
+            }[];
+            afterDisplayedRegionsSet(cb: Function): void;
+            horizontalScroll(distance: number): number;
+            center(): void;
+            showAllRegions(): void;
+            showAllRegionsInAssembly(assemblyName?: string): void;
+            setDraggingTrackId(idx?: string): void;
+            setScaleFactor(factor: number): void;
+            clearView(): void;
+            exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions): Promise<void>;
+        } & {
+            slide: (viewWidths: number) => void;
+        } & {
+            zoom: (targetBpPerPx: number) => void;
+        } & {
+            readonly canShowCytobands: boolean;
+            readonly showCytobands: boolean;
+            readonly anyCytobandsExist: boolean;
+            readonly cytobandOffset: number;
+        } & {
+            menuItems(): import("@jbrowse/core/ui").MenuItem[];
+        } & {
+            readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+            readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+            readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
+            readonly visibleLocStrings: string;
+            readonly coarseVisibleLocStrings: string;
+        } & {
+            setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
+            afterAttach(): void;
+        } & {
+            moveTo(start?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").BpOffset): void;
+            navToLocString(input: string, optAssemblyName?: string): Promise<void>;
+            navToSearchString({ input, assembly, }: {
+                input: string;
+                assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
+            }): Promise<void>;
+            navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
+            navTo(query: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").NavLocation): void;
+            navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").NavLocation[]): void;
+        } & {
+            rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            bpToPx({ refName, coord, regionNumber, }: {
+                refName: string;
+                coord: number;
+                regionNumber?: number;
+            }): {
+                index: number;
+                offsetPx: number;
+            } | undefined;
+            centerAt(coord: number, refName: string, regionNumber?: number): void;
+            pxToBp(px: number): {
+                coord: number;
+                index: number;
+                refName: string;
+                oob: boolean;
+                assemblyName: string;
+                offset: number;
+                start: number;
+                end: number;
+                reversed?: boolean;
+            };
+            readonly centerLineInfo: {
+                coord: number;
+                index: number;
+                refName: string;
+                oob: boolean;
+                assemblyName: string;
+                offset: number;
+                start: number;
+                end: number;
+                reversed?: boolean;
+            } | undefined;
+        } & {
+            afterCreate(): void;
+        }, 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").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
+            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]>;
+            showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        }>>, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    } & {
+        setClickedPosition(arg?: {
+            structureSeqPos: number;
+            code: string;
+            chain: string;
+        }): void;
+        setClickGenomeHighlights(r: import("@jbrowse/core/util").Region[]): void;
+        clearClickGenomeHighlights(): void;
+        setHoverGenomeHighlights(r: import("@jbrowse/core/util").Region[]): void;
+        clearHoverGenomeHighlights(): void;
+        setHoveredPosition(arg?: {
+            structureSeqPos?: number;
+            chain?: string;
+            code?: string;
+        }): void;
+        setAlignment(r?: import("../mappings").PairwiseAlignment): void;
+        setAlignmentStatus(str: string): void;
+    } & {
+        readonly structureSeqToTranscriptSeqPosition: Record<string, number> | undefined;
+        readonly transcriptSeqToStructureSeqPosition: Record<string, number> | undefined;
+        readonly structurePositionToAlignmentMap: Record<string, number> | undefined;
+        readonly transcriptPositionToAlignmentMap: Record<string, number> | undefined;
+        readonly pairwiseAlignmentToTranscriptPosition: Record<number, number> | undefined;
+        readonly pairwiseAlignmentToStructurePosition: Record<number, number> | undefined;
+        readonly clickString: string;
+        readonly hoverString: string;
+        readonly genomeToTranscriptSeqMapping: {
+            g2p: Record<number, number | undefined>;
+            p2g: Record<number, number | undefined>;
+            refName: string;
+            strand: number;
+        } | undefined;
+        readonly structureSeqHoverPos: number | undefined;
+        readonly exactMatch: boolean;
+        readonly zoomToBaseLevel: boolean;
+        readonly showHighlight: boolean;
+        readonly molstarPluginContext: PluginContext | undefined;
+    } & {
+        afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     showControls: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    feature: import("mobx-state-tree").IType<SimpleFeatureSerialized, SimpleFeatureSerialized, SimpleFeatureSerialized>;
-    seq1: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    seq2: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    alignment: import("mobx-state-tree").IType<{
-        consensus: string;
-        alns: {
-            id: any;
-            seq: any;
-        }[];
-    } | undefined, {
-        consensus: string;
-        alns: {
-            id: any;
-            seq: any;
-        }[];
-    } | undefined, {
-        consensus: string;
-        alns: {
-            id: any;
-            seq: any;
-        }[];
-    } | undefined>;
-    connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     showHighlight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     zoomToBaseLevel: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showAlignment: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -84,89 +518,32 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #volatile
      */
-    error: unknown;
-    /**
-     * #volatile
-     */
-    clickPosition: {
-        structureSeqPos: number;
-        code: string;
-        chain: string;
-    } | undefined;
+    progress: string;
     /**
      * #volatile
      */
-    hoverPosition: {
-        structureSeqPos: number;
-        code?: string;
-        chain?: string;
-    } | undefined;
+    error: unknown;
     /**
      * #volatile
      */
-    progress: string;
-} & {
-    /**
-     * #getter
-     */
-    readonly connectedView: MaybeLGV;
+    molstarPluginContext: PluginContext | undefined;
 } & {
     /**
      * #action
      */
-    setShowAlignment(f: boolean): void;
-    /**
-     * #action
-     */
-    setHoveredPosition(arg?: {
-        structureSeqPos: number;
-        chain?: string;
-        code?: string;
-    }): void;
+    setHeight(n: number): void;
     /**
      * #action
      */
-    setSeqs(str1?: string, str2?: string): void;
+    setShowAlignment(f: boolean): void;
     /**
      * #action
      */
     setShowControls(arg: boolean): void;
-    /**
-     * #action
-     */
-    setProgress(str: string): void;
-    /**
-     * #action
-     */
-    setClickedPosition(arg?: {
-        structureSeqPos: number;
-        code: string;
-        chain: string;
-    }): void;
-    /**
-     * #action
-     */
-    setClickGenomeHighlights(r: IRegion[]): void;
-    /**
-     * #action
-     */
-    clearClickGenomeHighlights(): void;
-    /**
-     * #action
-     */
-    setHoverGenomeHighlights(r: IRegion[]): void;
-    /**
-     * #action
-     */
-    clearHoverGenomeHighlights(): void;
     /**
      * #action
      */
     setError(e: unknown): void;
-    /**
-     * #action
-     */
-    setAlignment(r?: ReturnType<typeof parsePairwise>): void;
     /**
      * #action
      */
@@ -175,56 +552,15 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setZoomToBaseLevel(arg: boolean): void;
-} & {
-    /**
-     * #getter
-     */
-    readonly structureSeqToTranscriptSeqPosition: Record<string, number | undefined> | undefined;
-    /**
-     * #getter
-     */
-    readonly transcriptSeqToStructureSeqPosition: Record<string, number | undefined> | undefined;
     /**
-     * #getter
-     */
-    readonly structurePositionToAlignmentMap: Record<string, number | undefined> | undefined;
-    /**
-     * #getter
-     */
-    readonly transcriptPositionToAlignmentMap: Record<string, number | undefined> | undefined;
-    /**
-     * #getter
-     */
-    readonly alignmentToTranscriptPosition: any;
-    /**
-     * #getter
-     */
-    readonly alignmentToStructurePosition: any;
-    /**
-     * #getter
-     */
-    readonly clickString: string;
-    /**
-     * #getter
-     */
-    readonly hoverString: string;
-    /**
-     * #getter
-     */
-    readonly genomeToTranscriptSeqMapping: {
-        g2p: Record<number, number | undefined>;
-        p2g: Record<number, number | undefined>;
-        refName: string;
-        strand: number;
-    } | undefined;
-    /**
-     * #getter
+     * #action
      */
-    readonly structureSeqHoverPos: number | undefined;
-    readonly exactMatch: boolean;
+    setMolstarPluginContext(p?: PluginContext): void;
 } & {
     afterAttach(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
 export type JBrowsePluginProteinViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginProteinViewModel = Instance<JBrowsePluginProteinViewStateModel>;
+export type JBrowsePluginProteinStructureStateModel = typeof Structure;
+export type JBrowsePluginProteinStructureModel = Instance<JBrowsePluginProteinStructureStateModel>;