react-msaview 8.4.1 → 9.1.0

package/dist/svgTestUtil.d.ts

@@ -1,11 +1,11 @@
 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" | "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" | "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]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     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]>;
@@ -13,7 +13,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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" | "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]>;
@@ -397,17 +396,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    setTreeAreaWidth(n: number): void;
-    setTreeWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
+    setTreeWidth(n: number | undefined): void;
     setLabelsAlignRight(arg: boolean): void;
     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;
-    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -418,6 +415,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     headerHeight: number;
     hideHeader: boolean;
+    importForm: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -496,7 +494,6 @@ 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;
@@ -533,6 +530,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowNamesSet: Map<string, number>;
     readonly resolvedClades: import("./types.ts").ResolvedClade[];
     readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -543,7 +551,7 @@ 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;
@@ -566,6 +574,7 @@ 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[];
@@ -589,7 +598,6 @@ 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;
@@ -598,7 +606,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly totalWidth: number;
 } & {
     readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     readonly columnTrackContent: Map<string, {
         values?: number[];
@@ -609,9 +616,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     columnTrackModel(track: import("./types.ts").ColumnTrackSpec): import("./types.ts").BasicTrack;
     readonly columnTrackModels: import("./types.ts").BasicTrack[];
 } & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
@@ -679,17 +683,12 @@ 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;
     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;
@@ -782,15 +781,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(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;
     zoomToRegion(region: import("./types.ts").Region): void;
+    revealRegion(region: import("./types.ts").Region): void;
     zoomToSelection(): void;
     selectBlock(anchor: {
         col: number;
@@ -801,11 +802,11 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }): 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" | "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" | "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]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     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]>;
@@ -813,7 +814,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     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" | "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]>;
@@ -1197,17 +1197,15 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    setTreeAreaWidth(n: number): void;
-    setTreeWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
+    setTreeWidth(n: number | undefined): void;
     setLabelsAlignRight(arg: boolean): void;
     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;
-    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1218,6 +1216,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     headerHeight: number;
     hideHeader: boolean;
+    importForm: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -1296,7 +1295,6 @@ 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;
@@ -1333,6 +1331,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowNamesSet: Map<string, number>;
     readonly resolvedClades: import("./types.ts").ResolvedClade[];
     readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -1343,7 +1352,7 @@ 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;
@@ -1366,6 +1375,7 @@ 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[];
@@ -1389,7 +1399,6 @@ 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;
@@ -1398,7 +1407,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly totalWidth: number;
 } & {
     readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     readonly columnTrackContent: Map<string, {
         values?: number[];
@@ -1409,9 +1417,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     columnTrackModel(track: import("./types.ts").ColumnTrackSpec): import("./types.ts").BasicTrack;
     readonly columnTrackModels: import("./types.ts").BasicTrack[];
 } & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
@@ -1479,17 +1484,12 @@ 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;
     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;
@@ -1582,15 +1582,17 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(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;
     zoomToRegion(region: import("./types.ts").Region): void;
+    revealRegion(region: import("./types.ts").Region): void;
     zoomToSelection(): void;
     selectBlock(anchor: {
         col: number;
@@ -1609,8 +1611,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
@@ -1618,7 +1620,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks: import("./types.ts").ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
@@ -1747,8 +1748,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
@@ -1756,7 +1757,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;

package/dist/tipLabels.d.ts

@@ -0,0 +1,8 @@
+import type { NodeWithIds } from './types.ts';
+/** the leaf names of a tree, and its depth in levels from the root */
+export declare function treeTips(tree: NodeWithIds): {
+    names: string[];
+    depth: number;
+};
+/** the width of the widest label at `fontSize`, measuring the longest few */
+export declare function widestLabel(labels: string[], fontSize: number): number;

package/dist/tipLabels.js

@@ -0,0 +1,46 @@
+import { measureTextCanvas } from './measureTextCanvas.js';
+// A label's width follows its length closely enough that the widest one is
+// among the longest few, so a 230k-tip tree measures this many strings.
+const measuredLabels = 100;
+/** the leaf names of a tree, and its depth in levels from the root */
+export function treeTips(tree) {
+    const names = [];
+    let depth = 0;
+    const stack = [[tree, 0]];
+    for (let entry = stack.pop(); entry; entry = stack.pop()) {
+        const [node, level] = entry;
+        const { children } = node;
+        if (children.length > 0) {
+            for (const child of children) {
+                stack.push([child, level + 1]);
+            }
+        }
+        else {
+            names.push(node.name);
+            depth = Math.max(depth, level);
+        }
+    }
+    return { names, depth };
+}
+/** the width of the widest label at `fontSize`, measuring the longest few */
+export function widestLabel(labels, fontSize) {
+    const counts = [];
+    for (const label of labels) {
+        counts[label.length] = (counts[label.length] ?? 0) + 1;
+    }
+    let shortest = counts.length;
+    for (let seen = 0; shortest > 0 && seen < measuredLabels;) {
+        shortest--;
+        seen += counts[shortest] ?? 0;
+    }
+    let widest = 0;
+    let ties = 0;
+    for (const label of labels) {
+        if (label.length > shortest ||
+            (label.length === shortest && ties++ < measuredLabels)) {
+            widest = Math.max(widest, measureTextCanvas(label, fontSize));
+        }
+    }
+    return widest;
+}
+//# sourceMappingURL=tipLabels.js.map

package/dist/tipLabels.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"tipLabels.js","sourceRoot":"","sources":["../src/tipLabels.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAI1D,2EAA2E;AAC3E,wEAAwE;AACxE,MAAM,cAAc,GAAG,GAAG,CAAA;AAE1B,sEAAsE;AACtE,MAAM,UAAU,QAAQ,CAAC,IAAiB;IACxC,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAA4B,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IAClD,KAAK,IAAI,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,EAAE,CAAC;QACzD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QAC3B,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACzB,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,KAAK,MAAM,KAAK,IAAI,QAAQ,EAAE,CAAC;gBAC7B,KAAK,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC,CAAA;YAChC,CAAC;QACH,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAChC,CAAC;IACH,CAAC;IACD,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAA;AACzB,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CAAC,MAAgB,EAAE,QAAgB;IAC5D,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAA;IAC5B,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,QAAQ,GAAG,CAAC,IAAI,IAAI,GAAG,cAAc,GAAG,CAAC;QAC1D,QAAQ,EAAE,CAAA;QACV,IAAI,IAAI,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC/B,CAAC;IACD,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IACE,KAAK,CAAC,MAAM,GAAG,QAAQ;YACvB,CAAC,KAAK,CAAC,MAAM,KAAK,QAAQ,IAAI,IAAI,EAAE,GAAG,cAAc,CAAC,EACtD,CAAC;YACD,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,iBAAiB,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAC/D,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

package/dist/types.d.ts

@@ -44,7 +44,6 @@ export interface ArcTrackModel extends BasicTrackModel {
     arcColor?: string;
 }
 export interface BasicTrack {
-    ReactComponent: React.FC<any>;
     model: TextTrackModel & BarTrackModel & ArcTrackModel;
 }
 export interface ArcSpec {

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "8.4.1";
+export declare const version = "9.1.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '8.4.1';
+export const version = '9.1.0';
 //# sourceMappingURL=version.js.map

package/dist/viewerSnapshot.d.ts

@@ -0,0 +1,169 @@
+import type { MSAViewerProps } from './components/MSAViewer.tsx';
+import type { ColorScheme, Highlight } from './types.ts';
+export declare function colorSchemeSnapshot(scheme: ColorScheme | undefined): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+};
+/**
+ * The `highlightColumns` prop as `highlights`: one `{start, end}` per run of
+ * adjacent 1-based alignment columns
+ */
+export declare function columnHighlights(columns?: number[]): {
+    start: number;
+    end: number;
+}[];
+export declare function viewerHighlights({ highlights, highlightColumns, }: Pick<MSAViewerProps, 'highlights' | 'highlightColumns'>): Highlight[];
+/** each filehandle prop, or the URL prop standing in for it */
+export declare function fileLocations({ msaFilehandle, treeFilehandle, gffFilehandle, msaUrl, treeUrl, gffUrl, }: MSAViewerProps): {
+    msaFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+};
+export declare function resolveTheme(theme: MSAViewerProps['theme']): import("@mui/material").Theme;
+/**
+ * The model snapshot `MSAViewer` creates from its props. The CLI's `--props`
+ * reads the same JSON the R and Python widgets send, so a figure exported
+ * headlessly draws what the widget drew.
+ */
+export declare function viewerSnapshot(props: MSAViewerProps): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+};