react-msaview 6.5.0 → 8.0.0

package/dist/svgTestUtil.d.ts

@@ -1,7 +1,7 @@
 import MSAModelF from './model.ts';
 type Snapshot = NonNullable<Parameters<ReturnType<typeof MSAModelF>['create']>[0]>;
 export declare function installSvgTestEnv(contextExtras?: Partial<CanvasRenderingContext2D>): void;
-export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -9,22 +9,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -410,7 +414,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
     columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -424,10 +430,13 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         [k: string]: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
+    clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Clade, import("./types.ts").Clade, import("./types.ts").Clade>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Encoding, import("./types.ts").Encoding, import("./types.ts").Encoding>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").RowPanelSpec, import("./types.ts").RowPanelSpec, import("./types.ts").RowPanelSpec>>, [undefined]>;
 }> & {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
@@ -444,6 +453,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
     setDrawNodeBubbles(arg: boolean): void;
+    setDrawNodeLabels(arg: boolean): void;
+    setShowTreeOverview(arg: boolean): void;
+    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -452,9 +464,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -472,11 +484,13 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
+    transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    sequenceLogoTrackHeight: number;
     marginLeft: number;
     error: unknown;
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
@@ -488,9 +502,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
+    addWarning(warning: string): void;
+    clearWarnings(): void;
+    setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setClades(clades: import("./types.ts").Clade[]): void;
+    applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
+    clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -513,14 +533,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+    setGFF(result: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
-    extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
     readonly header: Record<string, unknown> | {
         info: string;
@@ -537,13 +558,18 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    readonly unshareableData: import("./types.ts").UnshareableData[];
     menuItems(): never[];
-    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
+    readonly rowData: Record<string, Record<string, string> | undefined>;
+    rowDataOf(name: string): Record<string, string> | undefined;
+    readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
+    readonly resolvedClades: import("./types.ts").ResolvedClade[];
+    readonly cladeGutterWidth: number;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -551,6 +577,21 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeOverviewHeight: number;
+    readonly treeOverviewLayout: {
+        root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+        numTips: number;
+        maxDepthToLeaf: number;
+        showBranchLen: boolean;
+    } | undefined;
+    readonly treeOverviewClades: import("./types.ts").ResolvedClade[];
+    readonly treeOverviewFocusRows: [number, number] | undefined;
+    treeOverviewHit(y: number): {
+        id: string;
+        rows: [number, number];
+    } | undefined;
+    readonly rowPanelsWidth: number;
+    readonly rowPanelsHeaderHeight: 0 | 56;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
@@ -560,7 +601,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -578,29 +619,87 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly rootToTipLength: number;
     readonly maxBranchLength: number;
+    readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
     readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("./types.ts").TrackKind, heightKey?: string, given?: number): number;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("./types.ts").BasicTrack[];
+    readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: import("./types.ts").Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
+    readonly residueMappingProblems: import("./types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: import("./types.ts").ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("./types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("./types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("./types.ts").RowResidue | undefined;
+} & {
+    readonly treeScaleBar: {
+        step: number;
+        px: number;
+        label: string;
+    } | undefined;
+    readonly topBandHeight: number;
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
 } & {
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
-    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
-    readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
+    readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
+    setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    replaceTree(newick: string): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -608,7 +707,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
-    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
@@ -617,44 +716,22 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    setRowData(rowData: Record<string, Record<string, string>>): void;
+    setEncodings(encodings: import("./types.ts").Encoding[]): void;
+    setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
+    setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
     setStatus(status?: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     }): void;
-} & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
-    readonly tracks: import("./types.ts").BasicTrack[];
-    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
-    readonly showHorizontalScrollbar: boolean;
-    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
-    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
-    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
-    globalColToVisibleCol(globalCol: number): number | undefined;
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
-    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-} & {
-    readonly msaAreaHeight: number;
-    readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
-} & {
-    readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
+    cellAt(visibleCol: number, rowIndex?: number): import("./types.ts").Cell;
+    readonly hoveredCell: import("./types.ts").Cell | undefined;
+    readonly clickedCell: import("./types.ts").Cell | undefined;
+    readonly viewport: import("./types.ts").Viewport | undefined;
     readonly segmentDomainTypes: import("msa-parsers").Annotation[];
     readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
     readonly fillPalette: {
@@ -663,8 +740,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly strokePalette: {
         [k: string]: string;
     };
+    readonly featureFillEncoding: import("./types.ts").ResolvedEncoding | undefined;
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
     readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly legends: import("./types.ts").Legend[];
+    readonly domainUnderline: boolean;
     readonly domainBands: Map<string, import("./types.ts").DomainBand[]>;
     readonly domainBandsByStart: Map<string, import("./types.ts").DomainBand[]>;
     readonly mouseOverDomains: import("msa-parsers").Annotation[];
@@ -675,39 +760,36 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         end: number;
     }[];
     readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
-    readonly mouseOverColumnStats: {
-        col: number;
-        total: number;
-        gaps: number;
-        gapFraction: number;
-        conservation: number;
-        propertyConservation: number | undefined;
-        consensusLetter: string;
-        consensusCount: number;
-        consensusFraction: number;
-        distribution: [string, number][];
-    } | undefined;
+    columnStatsAt(col: number): import("./columnStats.ts").ColumnStats | undefined;
+    readonly mouseOverColumnStats: import("./columnStats.ts").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
             name?: string;
             accession?: string;
             dbxref?: string;
         } | undefined;
-        treeMetadata: Record<string, string> | undefined;
+        rowData: Record<string, string> | undefined;
     };
+    readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
+    readonly featureAlignShifts: Map<string, Map<string, number>>;
+    readonly tipLabelColors: Map<string, string> | undefined;
+    readonly rowTints: (string | undefined)[] | undefined;
+    readonly branchColors: Map<string, string> | undefined;
 } & {
     setHeaderHeight(arg: number): void;
-    setConservationTrackHeight(arg: number): void;
-    setSequenceLogoTrackHeight(arg: number): void;
+    setHideHeader(arg: boolean): void;
+    treeOverviewClick(y: number): void;
+    setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
+    zoomToRegion(region: import("./types.ts").Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
-} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -715,22 +797,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1116,7 +1202,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
     columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec, import("./types.ts").ColumnTrackSpec>>, [undefined]>;
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping, import("./types.ts").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1130,10 +1218,13 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         [k: string]: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Highlight, import("./types.ts").Highlight, import("./types.ts").Highlight>>, [undefined]>;
+    clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Clade, import("./types.ts").Clade, import("./types.ts").Clade>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Encoding, import("./types.ts").Encoding, import("./types.ts").Encoding>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").RowPanelSpec, import("./types.ts").RowPanelSpec, import("./types.ts").RowPanelSpec>>, [undefined]>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
@@ -1150,6 +1241,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
     setDrawNodeBubbles(arg: boolean): void;
+    setDrawNodeLabels(arg: boolean): void;
+    setShowTreeOverview(arg: boolean): void;
+    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1158,9 +1252,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -1178,11 +1272,13 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
+    transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    sequenceLogoTrackHeight: number;
     marginLeft: number;
     error: unknown;
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
@@ -1194,9 +1290,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
+    addWarning(warning: string): void;
+    clearWarnings(): void;
+    setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setClades(clades: import("./types.ts").Clade[]): void;
+    applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
+    clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -1219,14 +1321,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+    setGFF(result: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
-    extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
     readonly header: Record<string, unknown> | {
         info: string;
@@ -1243,13 +1346,18 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    readonly unshareableData: import("./types.ts").UnshareableData[];
     menuItems(): never[];
-    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
+    readonly rowData: Record<string, Record<string, string> | undefined>;
+    rowDataOf(name: string): Record<string, string> | undefined;
+    readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
+    readonly resolvedClades: import("./types.ts").ResolvedClade[];
+    readonly cladeGutterWidth: number;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -1257,6 +1365,21 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeOverviewHeight: number;
+    readonly treeOverviewLayout: {
+        root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+        numTips: number;
+        maxDepthToLeaf: number;
+        showBranchLen: boolean;
+    } | undefined;
+    readonly treeOverviewClades: import("./types.ts").ResolvedClade[];
+    readonly treeOverviewFocusRows: [number, number] | undefined;
+    treeOverviewHit(y: number): {
+        id: string;
+        rows: [number, number];
+    } | undefined;
+    readonly rowPanelsWidth: number;
+    readonly rowPanelsHeaderHeight: 0 | 56;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
@@ -1266,7 +1389,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -1284,29 +1407,87 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly rootToTipLength: number;
     readonly maxBranchLength: number;
+    readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
     readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    readonly seqConsensus: string | undefined;
+    readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
+    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("./types.ts").TrackKind, heightKey?: string, given?: number): number;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
+    readonly basePairTrackModels: import("./types.ts").BasicTrack[];
+    readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly tracks: import("./types.ts").BasicTrack[];
+    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: import("./types.ts").Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
+    readonly residueMappingProblems: import("./types.ts").ResidueMappingProblem[];
+    readonly usableResidueMappings: import("./types.ts").ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("./types.ts").MappedStructure;
+    }[];
+    structureResidue(rowName: string, seqPos: number, structureId?: string): import("./types.ts").StructureResidue | undefined;
+    rowResidue(structureId: string, position: number, asymId?: string): import("./types.ts").RowResidue | undefined;
+} & {
+    readonly treeScaleBar: {
+        step: number;
+        px: number;
+        label: string;
+    } | undefined;
+    readonly topBandHeight: number;
+    readonly msaAreaHeight: number;
+    readonly totalTrackAreaHeight: number;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
 } & {
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
-    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
-    readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
+    readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
+    setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    replaceTree(newick: string): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -1314,7 +1495,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
-    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
@@ -1323,44 +1504,22 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("./types.ts").ColumnTrackSpec[]): void;
+    setRowData(rowData: Record<string, Record<string, string>>): void;
+    setEncodings(encodings: import("./types.ts").Encoding[]): void;
+    setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
+    setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
     setStatus(status?: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     }): void;
-} & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly adapterTrackModels: import("./types.ts").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
-    readonly tracks: import("./types.ts").BasicTrack[];
-    readonly turnedOnTracks: import("./types.ts").BasicTrack[];
-    readonly showHorizontalScrollbar: boolean;
-    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
-    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
-    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
-    globalColToVisibleCol(globalCol: number): number | undefined;
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
-    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-} & {
-    readonly msaAreaHeight: number;
-    readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
-} & {
-    readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
+    cellAt(visibleCol: number, rowIndex?: number): import("./types.ts").Cell;
+    readonly hoveredCell: import("./types.ts").Cell | undefined;
+    readonly clickedCell: import("./types.ts").Cell | undefined;
+    readonly viewport: import("./types.ts").Viewport | undefined;
     readonly segmentDomainTypes: import("msa-parsers").Annotation[];
     readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
     readonly fillPalette: {
@@ -1369,8 +1528,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly strokePalette: {
         [k: string]: string;
     };
+    readonly featureFillEncoding: import("./types.ts").ResolvedEncoding | undefined;
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
     readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly legends: import("./types.ts").Legend[];
+    readonly domainUnderline: boolean;
     readonly domainBands: Map<string, import("./types.ts").DomainBand[]>;
     readonly domainBandsByStart: Map<string, import("./types.ts").DomainBand[]>;
     readonly mouseOverDomains: import("msa-parsers").Annotation[];
@@ -1381,36 +1548,33 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         end: number;
     }[];
     readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
-    readonly mouseOverColumnStats: {
-        col: number;
-        total: number;
-        gaps: number;
-        gapFraction: number;
-        conservation: number;
-        propertyConservation: number | undefined;
-        consensusLetter: string;
-        consensusCount: number;
-        consensusFraction: number;
-        distribution: [string, number][];
-    } | undefined;
+    columnStatsAt(col: number): import("./columnStats.ts").ColumnStats | undefined;
+    readonly mouseOverColumnStats: import("./columnStats.ts").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
             name?: string;
             accession?: string;
             dbxref?: string;
         } | undefined;
-        treeMetadata: Record<string, string> | undefined;
+        rowData: Record<string, string> | undefined;
     };
+    readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
+    readonly featureAlignShifts: Map<string, Map<string, number>>;
+    readonly tipLabelColors: Map<string, string> | undefined;
+    readonly rowTints: (string | undefined)[] | undefined;
+    readonly branchColors: Map<string, string> | undefined;
 } & {
     setHeaderHeight(arg: number): void;
-    setConservationTrackHeight(arg: number): void;
-    setSequenceLogoTrackHeight(arg: number): void;
+    setHideHeader(arg: boolean): void;
+    treeOverviewClick(y: number): void;
+    setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
+    zoomToRegion(region: import("./types.ts").Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
@@ -1425,6 +1589,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showBranchLen: boolean;
     drawTree: boolean;
     drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
     autoTreeAreaWidth: boolean;
     columnTracks: import("./types.ts").ColumnTrackSpec[];
     id: string;
@@ -1436,6 +1603,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     type: "MsaView";
     drawMsaLetters: boolean;
     scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
     rowHeight: number;
     scrollY: number;
@@ -1525,10 +1693,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
+    residueMappings: import("./types.ts").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];
+    clades: import("./types.ts").Clade[];
+    encodings: import("./types.ts").Encoding[];
+    rowPanels: import("./types.ts").RowPanelSpec[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;
@@ -1547,6 +1720,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     showBranchLen: boolean;
     drawTree: boolean;
     drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
     autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
@@ -1558,6 +1734,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     type: "MsaView";
     drawMsaLetters: boolean;
     scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
     rowHeight: number;
     scrollY: number;
@@ -1647,10 +1824,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
+    residueMappings: import("./types.ts").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];
+    clades: import("./types.ts").Clade[];
+    encodings: import("./types.ts").Encoding[];
+    rowPanels: import("./types.ts").RowPanelSpec[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;