react-msaview 9.1.0 → 9.2.0

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<{}, "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]>;
@@ -405,6 +408,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -414,6 +418,11 @@ 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: {
@@ -421,6 +430,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         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;
@@ -494,8 +507,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly allAnnotations: import("msa-parsers").Annotation[];
-    readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
@@ -523,6 +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;
@@ -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[];
@@ -621,6 +635,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
     readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly referenceTrackModels: import("./types.ts").BasicTrack[];
     readonly tracks: import("./types.ts").BasicTrack[];
     readonly turnedOnTracks: import("./types.ts").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
@@ -654,7 +669,10 @@ 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;
@@ -667,6 +685,7 @@ 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[];
@@ -686,6 +705,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -698,6 +719,7 @@ 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;
@@ -781,6 +803,7 @@ 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;
@@ -789,7 +812,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -800,9 +823,9 @@ 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>>;
@@ -813,6 +836,7 @@ 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]>;
@@ -820,15 +844,17 @@ 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]>;
@@ -1206,6 +1232,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1215,6 +1242,11 @@ 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: {
@@ -1222,6 +1254,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
+    zoomSnapshot: import("./zoomSnapshot.ts").ZoomSnapshot | undefined;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -1252,6 +1285,7 @@ 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;
@@ -1268,6 +1302,8 @@ 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;
@@ -1295,8 +1331,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly allAnnotations: import("msa-parsers").Annotation[];
-    readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
@@ -1324,6 +1358,8 @@ 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;
@@ -1387,6 +1423,7 @@ 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[];
@@ -1422,6 +1459,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
     readonly computedTrackModels: import("./types.ts").BasicTrack[];
+    readonly referenceTrackModels: import("./types.ts").BasicTrack[];
     readonly tracks: import("./types.ts").BasicTrack[];
     readonly turnedOnTracks: import("./types.ts").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
@@ -1455,7 +1493,10 @@ 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;
@@ -1468,6 +1509,7 @@ 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[];
@@ -1487,6 +1529,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -1499,6 +1543,7 @@ 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;
@@ -1582,6 +1627,7 @@ 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;
@@ -1590,7 +1636,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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;
@@ -1601,7 +1647,7 @@ 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;
@@ -1619,16 +1665,19 @@ 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;
@@ -1756,16 +1805,19 @@ 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];

package/dist/treeDisplay.js

@@ -0,0 +1,209 @@
+import { generateNodeIds, parseEmfTree, parseNewick } from 'msa-parsers';
+import { cladeHighlightAlpha, cladeHighlightColor } from './constants.js';
+import { flatToTree } from './flatToTree.js';
+import { collapse, find, forEachDescendant, hierarchy, leafIndex, leaves, mrca, sort, sum as hierarchySum, } from './hierarchy.js';
+import { parseAsn1 } from './parseAsn1.js';
+import { midpointRoot, preorder, rerootTree } from './rerootTree.js';
+import { withAlpha } from './util.js';
+export function parseTreeText(text) {
+    if (text.startsWith('BioTreeContainer')) {
+        return flatToTree(parseAsn1(text));
+    }
+    return parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text);
+}
+// the marks that set tree state from a node rather than drawing
+const seedingMarks = new Set(['collapse', 'focus', 'rotate']);
+/**
+ * Each tip of the full tree in the order the tree draws it, with the on-screen
+ * row that shows it: its own, or the row of the collapsed node standing for it
+ */
+function tipRows(root) {
+    const rows = new Map();
+    let row = 0;
+    const pushReversed = (stack, nodes) => {
+        for (let i = nodes.length - 1; i >= 0; i--) {
+            stack.push(nodes[i]);
+        }
+    };
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        if (node.children?.length) {
+            pushReversed(stack, node.children);
+        }
+        else {
+            const hidden = [node];
+            while (hidden.length > 0) {
+                const tip = hidden.pop();
+                const kids = tip.children ?? tip._children;
+                if (kids?.length) {
+                    pushReversed(hidden, kids);
+                }
+                else {
+                    rows.set(tip.data.name, { order: rows.size, row });
+                }
+            }
+            row++;
+        }
+    }
+    return rows;
+}
+/**
+ * The rows a clade covers and the node an `mrca` names, or undefined when the
+ * clade does not resolve: a tip name the tree does not have or has twice, or a
+ * leaf count `tips` disagrees with. A `range` counts its tips in the order
+ * `tips` gives them, so a collapsed clade inside it counts every leaf it
+ * stands for. `index` is the memoized leaf pass over the tree.
+ */
+function cladeRows(clade, root, index, tips) {
+    if (clade.range) {
+        const [a, b] = clade.range.map(name => index.get(name) ? tips.get(name) : undefined);
+        if (a === undefined || b === undefined) {
+            return undefined;
+        }
+        const [first, last] = a.order <= b.order ? [a, b] : [b, a];
+        return last.order - first.order + 1 === clade.tips
+            ? { rows: [first.row, last.row] }
+            : undefined;
+    }
+    const node = clade.mrca ? mrca(root, clade.mrca, index) : undefined;
+    if (!node) {
+        return undefined;
+    }
+    const nodeTips = leaves(node);
+    if (nodeTips.length !== clade.tips) {
+        return undefined;
+    }
+    let first = Infinity;
+    let last = -Infinity;
+    for (const tip of nodeTips) {
+        const row = tips.get(tip.data.name)?.row;
+        if (row !== undefined) {
+            first = Math.min(first, row);
+            last = Math.max(last, row);
+        }
+    }
+    return first <= last
+        ? { rows: [first, last], nodeId: node.data.id }
+        : undefined;
+}
+/**
+ * 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 function resolveClades(clades, root, displayed) {
+    const index = leafIndex(root);
+    const tips = tipRows(displayed);
+    return clades.flatMap(clade => {
+        const resolved = cladeRows(clade, root, index, tips);
+        const seeding = seedingMarks.has(clade.mark);
+        return resolved && !(seeding && resolved.nodeId === undefined)
+            ? [
+                {
+                    ...resolved,
+                    mark: clade.mark,
+                    color: withAlpha(clade.color ?? cladeHighlightColor, cladeHighlightAlpha),
+                    markColor: clade.color,
+                    label: clade.label,
+                },
+            ]
+            : [];
+    });
+}
+const childOrders = {
+    input: undefined,
+    branchLength: (a, b) => (a.data.length ?? 1) - (b.data.length ?? 1),
+    ladderize: (a, b) => a.value - b.value,
+    ladderizeReverse: (a, b) => b.value - a.value,
+};
+/**
+ * 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 function buildTreeRoot(tree, { collapsed, rotated, order, showOnly, }) {
+    let hier = hierarchy(tree, d => d.children);
+    hierarchySum(hier, d => (d.children.length > 0 ? 0 : 1));
+    const compare = childOrders[order];
+    if (compare) {
+        sort(hier, compare);
+    }
+    if (rotated.length > 0) {
+        const flip = new Set(rotated);
+        forEachDescendant(hier, n => {
+            if (flip.has(n.data.id)) {
+                n.children?.reverse();
+            }
+        });
+    }
+    if (showOnly) {
+        const res = find(hier, n => n.data.id === showOnly);
+        if (res) {
+            hier = res;
+        }
+    }
+    for (const collapsedId of collapsed) {
+        const node = find(hier, n => n.data.id === collapsedId);
+        if (node) {
+            if (node.children) {
+                collapse(node);
+            }
+            else if (node.parent?.children) {
+                node.parent.children = node.parent.children.filter(c => c.data.id !== collapsedId);
+            }
+        }
+    }
+    return hier;
+}
+/**
+ * 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 function outgroupNode(root, outgroup) {
+    const index = leafIndex(root);
+    const node = mrca(root, outgroup, index);
+    if (node !== root) {
+        return node;
+    }
+    const out = new Set(outgroup);
+    const rest = leaves(root)
+        .map(n => n.data.name)
+        .filter(name => !out.has(name));
+    const other = mrca(root, rest, index);
+    return other === root ? undefined : other;
+}
+/**
+ * `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 function rootTree(tree, treeRoot) {
+    const plain = new Map();
+    for (const node of preorder(tree).reverse()) {
+        plain.set(node, {
+            name: node.name === node.id ? undefined : node.name,
+            length: node.length,
+            children: node.children.map(c => plain.get(c)),
+        });
+    }
+    const input = plain.get(tree);
+    if (treeRoot === 'midpoint') {
+        return generateNodeIds(midpointRoot(input));
+    }
+    const target = outgroupNode(hierarchy(tree, d => d.children), treeRoot.outgroup);
+    return target
+        ? generateNodeIds(rerootTree(input, plain.get(target.data)))
+        : tree;
+}
+// the inclusive tip indices a node covers, from its xMin/xMax in a layout one
+// row per tip
+export function tipRange(node) {
+    return [Math.round(node.xMin - 0.5), Math.round(node.xMax - 0.5)];
+}
+//# sourceMappingURL=treeDisplay.js.map

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