react-msaview 8.2.0 → 8.4.0

package/dist/svgTestUtil.d.ts

@@ -1,24 +1,26 @@
 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" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "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" | "treeOrder" | "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]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("./types.ts").TreeOrder>, [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" | "colorSchemeName" | "customColorScheme" | "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]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, 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" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "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]>;
@@ -412,6 +414,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | 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]>;
@@ -434,6 +438,8 @@ 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]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Feature, import("./types.ts").Feature, import("./types.ts").Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").MsaSelection | undefined, import("./types.ts").MsaSelection | undefined, import("./types.ts").MsaSelection | undefined>;
     region: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Region | undefined, import("./types.ts").Region | undefined, import("./types.ts").Region | 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]>;
@@ -453,6 +459,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawTree(arg: boolean): void;
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: import("./types.ts").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
@@ -460,6 +467,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
@@ -489,7 +497,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     minimapHeight: number;
     marginLeft: number;
     error: unknown;
-    warnings: string[];
+    loadWarnings: string[];
+    dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
@@ -504,12 +513,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
     setRegion(region?: import("./types.ts").Region): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setFeatures(features: import("./types.ts").Feature[]): void;
+    setSelection(selection?: import("./types.ts").MsaSelection): void;
+    clearSelection(): void;
     setClades(clades: import("./types.ts").Clade[]): void;
     applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
     clearHighlight(owner: string): void;
@@ -521,6 +532,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setColWidth(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: import("./types.ts").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -535,16 +549,18 @@ 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;
+    setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
     readonly colorScheme: Record<string, string>;
+    readonly dynamicColorSchemeName: string | undefined;
     readonly header: Record<string, unknown> | {
         info: string;
         version: string | undefined;
@@ -567,6 +583,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
+    readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
@@ -579,6 +596,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
         root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
@@ -618,9 +636,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
-    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly treeLayout: {
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
+        leaves: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
     readonly totalHeight: number;
-    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
     readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
@@ -646,7 +669,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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 basePairTrackModels: import("./types.ts").BasicTrack[];
@@ -660,6 +682,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     globalColToVisibleCol(globalCol: number): number | undefined;
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(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;
@@ -692,19 +715,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
-    readonly maxScrollX: number;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
     readonly maxScrollY: number;
     readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
     setScrollZoom(arg: boolean): void;
     setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -720,7 +750,7 @@ 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;
+    setRowData(rowData: import("./types.ts").RowDataInput): void;
     setEncodings(encodings: import("./types.ts").Encoding[]): void;
     setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
@@ -730,8 +760,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         onCancel?: () => void;
     }): void;
 } & {
-    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;
@@ -762,6 +790,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[];
     fillHighlightLabel(label: string, row?: string, start?: number): string;
     readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
+    readonly resolvedSelection: import("./types.ts").ResolvedSelection | undefined;
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    readonly selectionFasta: string;
     columnStatsAt(col: number): import("./columnStats.ts").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
@@ -772,6 +810,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
     readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
     readonly tipLabelColors: Map<string, string> | undefined;
@@ -784,30 +842,41 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     zoomToRegion(region: import("./types.ts").Region): void;
+    zoomToSelection(): void;
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
     fitHorizontally(): void;
     afterCreate(): void;
-} & 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"> & {
+} & 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" | "treeOrder" | "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]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("./types.ts").TreeOrder>, [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" | "colorSchemeName" | "customColorScheme" | "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]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, 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" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "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]>;
@@ -1201,6 +1270,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | 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]>;
@@ -1223,6 +1294,8 @@ 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]>;
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Feature, import("./types.ts").Feature, import("./types.ts").Feature>>, [undefined]>;
+    selection: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").MsaSelection | undefined, import("./types.ts").MsaSelection | undefined, import("./types.ts").MsaSelection | undefined>;
     region: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").Region | undefined, import("./types.ts").Region | undefined, import("./types.ts").Region | 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]>;
@@ -1242,6 +1315,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawTree(arg: boolean): void;
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: import("./types.ts").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
@@ -1249,6 +1323,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
@@ -1278,7 +1353,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     minimapHeight: number;
     marginLeft: number;
     error: unknown;
-    warnings: string[];
+    loadWarnings: string[];
+    dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
@@ -1293,12 +1369,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
     setRegion(region?: import("./types.ts").Region): void;
     setHighlights(highlights: import("./types.ts").Highlight[]): void;
+    setFeatures(features: import("./types.ts").Feature[]): void;
+    setSelection(selection?: import("./types.ts").MsaSelection): void;
+    clearSelection(): void;
     setClades(clades: import("./types.ts").Clade[]): void;
     applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
     clearHighlight(owner: string): void;
@@ -1310,6 +1388,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setColWidth(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: import("./types.ts").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -1324,16 +1405,18 @@ 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;
+    setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
     readonly colorScheme: Record<string, string>;
+    readonly dynamicColorSchemeName: string | undefined;
     readonly header: Record<string, unknown> | {
         info: string;
         version: string | undefined;
@@ -1356,6 +1439,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
+    readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
@@ -1368,6 +1452,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
         root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
@@ -1407,9 +1492,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
-    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly treeLayout: {
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
+        leaves: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
     readonly totalHeight: number;
-    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
     readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
@@ -1435,7 +1525,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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 basePairTrackModels: import("./types.ts").BasicTrack[];
@@ -1449,6 +1538,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     globalColToVisibleCol(globalCol: number): number | undefined;
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(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;
@@ -1481,19 +1571,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
-    readonly maxScrollX: number;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
     readonly maxScrollY: number;
     readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
     setScrollZoom(arg: boolean): void;
     setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -1509,7 +1606,7 @@ 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;
+    setRowData(rowData: import("./types.ts").RowDataInput): void;
     setEncodings(encodings: import("./types.ts").Encoding[]): void;
     setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
@@ -1519,8 +1616,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         onCancel?: () => void;
     }): void;
 } & {
-    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;
@@ -1551,6 +1646,16 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }[];
     fillHighlightLabel(label: string, row?: string, start?: number): string;
     readonly resolvedHighlights: import("./types.ts").ResolvedHighlight[];
+    readonly resolvedSelection: import("./types.ts").ResolvedSelection | undefined;
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    readonly selectionFasta: string;
     columnStatsAt(col: number): import("./columnStats.ts").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
@@ -1561,6 +1666,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
     readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
     readonly tipLabelColors: Map<string, string> | undefined;
@@ -1573,15 +1698,25 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     zoomToRegion(region: import("./types.ts").Region): void;
+    zoomToSelection(): void;
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
     fitHorizontally(): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
@@ -1589,6 +1724,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1693,6 +1829,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("./types.ts").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
@@ -1701,6 +1839,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];
+    features: import("./types.ts").Feature[];
+    selection: import("./types.ts").MsaSelection | undefined;
     region: import("./types.ts").Region | undefined;
     clades: import("./types.ts").Clade[];
     encodings: import("./types.ts").Encoding[];
@@ -1714,6 +1854,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } | {
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
@@ -1721,6 +1862,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1825,6 +1967,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("./types.ts").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
@@ -1833,6 +1977,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("./types.ts").Highlight[];
+    features: import("./types.ts").Feature[];
+    selection: import("./types.ts").MsaSelection | undefined;
     region: import("./types.ts").Region | undefined;
     clades: import("./types.ts").Clade[];
     encodings: import("./types.ts").Encoding[];