react-msaview 9.0.0 → 9.1.1

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<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "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").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -12,6 +12,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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]>;
+    showTreeScaleBar: 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]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -19,15 +20,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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" | "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"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "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]>;
+    domainFill: 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").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    embeddedMode: 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]>;
@@ -405,7 +408,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setOverviewHeight(n: number): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -415,12 +418,19 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    settingsOpen: boolean;
+    zoomHeld: {
+        col: number;
+        row: number;
+    };
     hideHeader: boolean;
+    importForm: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
+    zoomSnapshot: import("./zoomSnapshot.ts").ZoomSnapshot | undefined;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -451,6 +461,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
+    setSettingsOpen(arg: boolean): void;
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
@@ -467,6 +478,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
     clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
+    setDomainFill(arg: boolean): void;
+    setCellFill(mode: 'residue' | 'domain' | 'none'): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -494,9 +507,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -524,6 +534,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
     readonly numColumns: number;
     readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
@@ -552,7 +564,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
-        root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -575,6 +587,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rows: [string, string][];
     readonly numRows: number;
     seqPosIndex(rowName: string): Int32Array | undefined;
+    rowSequence(name: string): string | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -586,6 +599,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         color: string | undefined;
     }[];
     readonly colClustalX: Record<string, string>[];
+    readonly colSimilarity: Record<string, string>[];
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
@@ -598,7 +612,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
-    readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
@@ -655,7 +668,10 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly defaultOffAccessions: Set<string>;
+    featureOff(accession: string): boolean;
     readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly cellFill: 'residue' | 'domain' | 'none';
     readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
@@ -668,6 +684,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly msaCanvasWidth: number;
     readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
+    readonly wheelZooming: boolean;
     readonly isLoading: boolean;
     readonly dataWarnings: string[];
     readonly warnings: string[];
@@ -684,17 +701,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     replaceTree(newick: string): void;
     resetZoom(): void;
     zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
-    zoomOutHorizontal(): void;
-    zoomInHorizontal(): void;
-    zoomInVertical(): void;
-    zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
+    wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    endWheelZoom(): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
-    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -704,6 +718,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
+    setTracksShown(ids: string[], shown: boolean): void;
     setStatus(status?: {
         msg: string;
         onCancel?: () => void;
@@ -787,15 +802,18 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(arg: boolean): void;
+    setEmbeddedMode(arg: boolean): void;
+    setImportForm(arg: boolean): void;
     treeOverviewClick(y: number): void;
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
-    exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportSVG(opts: import("./exportLayout.ts").ExportSvgOptions): Promise<void>;
     exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
-    fitVertically(): void;
+    fitVertically(maxRowHeight?: any): void;
     zoomToRegion(region: import("./types.ts").Region): void;
+    revealRegion(region: import("./types.ts").Region): void;
     zoomToSelection(): void;
     selectBlock(anchor: {
         col: number;
@@ -804,9 +822,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         col: number;
         row?: number;
     }): void;
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
-} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "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").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -817,6 +835,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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]>;
+    showTreeScaleBar: 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]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -824,15 +843,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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" | "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"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "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]>;
+    domainFill: 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").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    embeddedMode: 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]>;
@@ -1210,7 +1231,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setOverviewHeight(n: number): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1220,12 +1241,19 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    settingsOpen: boolean;
+    zoomHeld: {
+        col: number;
+        row: number;
+    };
     hideHeader: boolean;
+    importForm: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
+    zoomSnapshot: import("./zoomSnapshot.ts").ZoomSnapshot | undefined;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -1256,6 +1284,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
+    setSettingsOpen(arg: boolean): void;
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
@@ -1272,6 +1301,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     applyHighlight(owner: string, highlights: import("./types.ts").Highlight[]): void;
     clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
+    setDomainFill(arg: boolean): void;
+    setCellFill(mode: 'residue' | 'domain' | 'none'): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -1299,9 +1330,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -1329,6 +1357,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
     readonly numColumns: number;
     readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
@@ -1357,7 +1387,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
-        root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -1380,6 +1410,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rows: [string, string][];
     readonly numRows: number;
     seqPosIndex(rowName: string): Int32Array | undefined;
+    rowSequence(name: string): string | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -1391,6 +1422,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         color: string | undefined;
     }[];
     readonly colClustalX: Record<string, string>[];
+    readonly colSimilarity: Record<string, string>[];
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
@@ -1403,7 +1435,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly totalHeight: number;
     readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
-    readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
@@ -1460,7 +1491,10 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly defaultOffAccessions: Set<string>;
+    featureOff(accession: string): boolean;
     readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly cellFill: 'residue' | 'domain' | 'none';
     readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
@@ -1473,6 +1507,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly msaCanvasWidth: number;
     readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
+    readonly wheelZooming: boolean;
     readonly isLoading: boolean;
     readonly dataWarnings: string[];
     readonly warnings: string[];
@@ -1489,17 +1524,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     replaceTree(newick: string): void;
     resetZoom(): void;
     zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
-    zoomOutHorizontal(): void;
-    zoomInHorizontal(): void;
-    zoomInVertical(): void;
-    zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
+    wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    endWheelZoom(): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
-    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -1509,6 +1541,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setRowPanels(panels: import("./types.ts").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("./types.ts").ResidueMapping[]): void;
     toggleTrack(id: string): void;
+    setTracksShown(ids: string[], shown: boolean): void;
     setStatus(status?: {
         msg: string;
         onCancel?: () => void;
@@ -1592,15 +1625,18 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(arg: boolean): void;
+    setEmbeddedMode(arg: boolean): void;
+    setImportForm(arg: boolean): void;
     treeOverviewClick(y: number): void;
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
-    exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportSVG(opts: import("./exportLayout.ts").ExportSvgOptions): Promise<void>;
     exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
-    fitVertically(): void;
+    fitVertically(maxRowHeight?: any): void;
     zoomToRegion(region: import("./types.ts").Region): void;
+    revealRegion(region: import("./types.ts").Region): void;
     zoomToSelection(): void;
     selectBlock(anchor: {
         col: number;
@@ -1609,7 +1645,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         col: number;
         row?: number;
     }): void;
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
@@ -1627,16 +1663,19 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks: import("./types.ts").ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
@@ -1764,16 +1803,19 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;

package/dist/treeDisplay.d.ts

@@ -0,0 +1,37 @@
+import type { HierarchyNode } from './hierarchy.ts';
+import type { Clade, NodeWithIds, ResolvedClade, TreeOrder, TreeRoot } from './types.ts';
+export declare function parseTreeText(text: string): import("@gmod/newick").NewickNode;
+/**
+ * Every clade that resolves, with its fill color settled, against the rows of
+ * `displayed`, the tree as drawn. The tree panel resolves against the
+ * displayed rows and the overview against its own, so both take the tree they
+ * draw. A `range` record names no node, so the seeding marks, which need one,
+ * drop it.
+ */
+export declare function resolveClades(clades: Clade[], root: HierarchyNode<NodeWithIds>, displayed: HierarchyNode<NodeWithIds>): ResolvedClade[];
+/**
+ * The tree with the display transforms applied: leaf counts summed, children
+ * put in `order` and each `rotated` node's reversed, `showOnly` taken as the
+ * new root, and each `collapsed` clade folded. The overview builds the same
+ * tree without the focus, so it shows the focused subtree inside the whole.
+ */
+export declare function buildTreeRoot(tree: NodeWithIds, { collapsed, rotated, order, showOnly, }: {
+    collapsed: readonly string[];
+    rotated: readonly string[];
+    order: TreeOrder;
+    showOnly?: string;
+}): HierarchyNode<NodeWithIds>;
+/**
+ * The node whose branch an outgroup roots the tree on: the outgroup's most
+ * recent common ancestor, or the rest of the tips' where that ancestor is the
+ * root, since the outgroup then straddles the root and the branch above the
+ * other side is the same branch of the unrooted tree.
+ */
+export declare function outgroupNode(root: HierarchyNode, outgroup: string[]): HierarchyNode<NodeWithIds> | undefined;
+/**
+ * `tree` rerooted as `treeRoot` asks, with fresh path ids. The ids of the tree
+ * as written become names on unnamed nodes, and a rerooting would carry them
+ * along as labels, so they come off first.
+ */
+export declare function rootTree(tree: NodeWithIds, treeRoot: TreeRoot): import("msa-parsers").NodeWithIds;
+export declare function tipRange(node: HierarchyNode): [number, number];