react-msaview 7.0.0 → 8.1.0

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" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "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]>;
@@ -410,6 +414,7 @@ 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<{
@@ -429,6 +434,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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][];
 } & {
@@ -445,6 +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;
@@ -453,6 +464,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -474,10 +486,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     highlightedColumns: number[] | undefined;
     transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    columnTrackHeights: Record<string, number>;
-    sequenceLogoTrackHeight: number;
-    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
     warnings: string[];
@@ -500,6 +508,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -551,12 +560,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -564,6 +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[];
@@ -602,6 +630,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     readonly showMsaLetters: boolean;
     readonly showTreeText: boolean;
+} & {
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("./types.ts").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: import("./types.ts").ColumnTrackSpec): import("./types.ts").BasicTrack;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
 } & {
     readonly labelWidthMap: Map<string, number>;
     readonly labelWidthScale: number;
@@ -610,12 +647,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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[];
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
     readonly computedTrackModels: import("./types.ts").BasicTrack[];
     readonly tracks: import("./types.ts").BasicTrack[];
@@ -628,6 +659,10 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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: {
@@ -637,6 +672,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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>;
@@ -653,9 +694,11 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
+    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;
@@ -666,7 +709,7 @@ 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;
@@ -675,6 +718,9 @@ 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?: {
@@ -684,16 +730,25 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     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: {
         [x: string]: string;
     };
-    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[];
@@ -704,40 +759,35 @@ 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;
     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;
-    setColumnTrackHeight(id: string, height: number): void;
-    setSequenceLogoTrackHeight(arg: number): void;
-    setArcTrackHeight(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>;
     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]>;
@@ -745,22 +795,26 @@ 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" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "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]>;
@@ -1146,6 +1200,7 @@ 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<{
@@ -1165,6 +1220,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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][];
 } & {
@@ -1181,6 +1239,9 @@ 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;
@@ -1189,6 +1250,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -1210,10 +1272,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     highlightedColumns: number[] | undefined;
     transientHighlights: Record<string, import("./types.ts").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    columnTrackHeights: Record<string, number>;
-    sequenceLogoTrackHeight: number;
-    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
     warnings: string[];
@@ -1236,6 +1294,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -1287,12 +1346,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -1300,6 +1363,21 @@ 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[];
@@ -1338,6 +1416,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     readonly showMsaLetters: boolean;
     readonly showTreeText: boolean;
+} & {
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("./types.ts").Arc[];
+    }>;
+    trackHeight(kind: import("./types.ts").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: import("./types.ts").ColumnTrackSpec): import("./types.ts").BasicTrack;
+    readonly columnTrackModels: import("./types.ts").BasicTrack[];
 } & {
     readonly labelWidthMap: Map<string, number>;
     readonly labelWidthScale: number;
@@ -1346,12 +1433,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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[];
-    }>;
-    readonly columnTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
     readonly computedTrackModels: import("./types.ts").BasicTrack[];
     readonly tracks: import("./types.ts").BasicTrack[];
@@ -1364,6 +1445,10 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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: {
@@ -1373,6 +1458,12 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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>;
@@ -1389,9 +1480,11 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
+    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;
@@ -1402,7 +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;
@@ -1411,6 +1504,9 @@ 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?: {
@@ -1420,16 +1516,25 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     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: {
         [x: string]: string;
     };
-    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[];
@@ -1440,37 +1545,32 @@ 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;
     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;
-    setColumnTrackHeight(id: string, height: number): void;
-    setSequenceLogoTrackHeight(arg: number): void;
-    setArcTrackHeight(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>;
     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, {
@@ -1485,6 +1585,9 @@ 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;
@@ -1496,6 +1599,7 @@ 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;
@@ -1585,11 +1689,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: 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;
@@ -1608,6 +1716,9 @@ 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;
@@ -1619,6 +1730,7 @@ 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;
@@ -1708,11 +1820,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: 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;