react-msaview 8.2.0 → 8.3.0

package/dist/rerootTree.js

@@ -0,0 +1,144 @@
+function preorder(root) {
+    const order = [];
+    const parents = new Map();
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        order.push(node);
+        for (const child of (node.children ?? [])) {
+            parents.set(child, node);
+            stack.push(child);
+        }
+    }
+    return { order, parents };
+}
+function hasLengths(order) {
+    return order.some(n => n.length !== undefined);
+}
+// the root's two children make one branch of the unrooted tree, which is the
+// branch a rerooting at either of them splits
+function mergedSibling(root, target) {
+    return root.children?.length === 2
+        ? root.children.find(c => c !== target)
+        : undefined;
+}
+/**
+ * The tree rooted on the branch above `target`, `offset` up from it, or at the
+ * middle of that branch without one. Where the root has two children, their
+ * branches are one branch of the unrooted tree, and `offset` runs across both.
+ *
+ * The nodes between `target` and the old root turn over. A name on one of them
+ * labels the branch above it, which is where a support value sits, so the name
+ * follows that branch to the node now at its lower end. A two-child root has
+ * nothing left to split once one child leaves, so it drops out and its
+ * branches join.
+ */
+export function rerootTree(root, target, offset) {
+    const { order, parents } = preorder(root);
+    if (!parents.has(target)) {
+        return root;
+    }
+    const lengths = hasLengths(order);
+    const sibling = parents.get(target) === root ? mergedSibling(root, target) : undefined;
+    const branch = (target.length ?? 0) + (sibling?.length ?? 0);
+    const at = Math.min(Math.max(offset ?? branch / 2, 0), branch);
+    const length = (n) => (lengths ? n : undefined);
+    const path = [target];
+    for (let n = parents.get(target); n; n = parents.get(n)) {
+        path.push(n);
+    }
+    // Built from the old root down, so the node each turned node now hangs
+    // `above` it already exists. undefined where the old root dropped out.
+    let above;
+    for (let i = path.length - 1; i >= 1; i--) {
+        const node = path[i];
+        const below = path[i - 1];
+        const children = node.children.filter(c => c !== below);
+        if (above) {
+            children.push(above);
+        }
+        if (children.length === 0) {
+            above = undefined;
+        }
+        else if (i === path.length - 1 && children.length === 1) {
+            const only = children[0];
+            above = {
+                ...only,
+                length: length((only.length ?? 0) + (below.length ?? 0) - (i === 1 ? at : 0)),
+            };
+        }
+        else {
+            above = {
+                ...node,
+                name: i === 1 ? undefined : below.name,
+                children,
+                length: length((below.length ?? 0) - (i === 1 ? at : 0)),
+            };
+        }
+    }
+    return {
+        children: [{ ...target, length: length(at) }, ...(above ? [above] : [])],
+    };
+}
+/**
+ * The tree rooted halfway along the longest path between two tips, which is
+ * where a clock would put the root: the usual choice for the unrooted tree
+ * FastTree, IQ-TREE or neighbor joining writes. A tree with no branch lengths
+ * counts branches.
+ */
+export function midpointRoot(root) {
+    const { order, parents } = preorder(root);
+    const tips = order.filter(n => !n.children?.length);
+    if (tips.length < 2) {
+        return root;
+    }
+    const lengths = hasLengths(order);
+    const weight = (n) => (lengths ? (n.length ?? 0) : 1);
+    // distance from `from` to every node over the unrooted tree, and the
+    // neighbor each was reached through
+    function reach(from) {
+        const dist = new Map([[from, 0]]);
+        const via = new Map();
+        const stack = [from];
+        while (stack.length > 0) {
+            const node = stack.pop();
+            const d = dist.get(node);
+            const parent = parents.get(node);
+            if (parent && !dist.has(parent)) {
+                dist.set(parent, d + weight(node));
+                via.set(parent, node);
+                stack.push(parent);
+            }
+            for (const child of (node.children ?? [])) {
+                if (!dist.has(child)) {
+                    dist.set(child, d + weight(child));
+                    via.set(child, node);
+                    stack.push(child);
+                }
+            }
+        }
+        return { dist, via };
+    }
+    function farthest(dist) {
+        return tips.reduce((best, tip) => dist.get(tip) > dist.get(best) ? tip : best);
+    }
+    const a = farthest(reach(tips[0]).dist);
+    const { dist, via } = reach(a);
+    const b = farthest(dist);
+    if (b === a) {
+        return root;
+    }
+    const half = dist.get(b) / 2;
+    let node = b;
+    let next = via.get(node);
+    while (dist.get(next) > half) {
+        node = next;
+        next = via.get(node);
+    }
+    // the midpoint lies on the branch between `node` and `next`, and whichever
+    // of them is the child carries that branch
+    return parents.get(node) === next
+        ? rerootTree(root, node, dist.get(node) - half)
+        : rerootTree(root, next, half - dist.get(next));
+}
+//# sourceMappingURL=rerootTree.js.map

package/dist/rerootTree.js.map

@@ -0,0 +1 @@
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package/dist/svgTestUtil.d.ts

@@ -1,12 +1,13 @@
 import MSAModelF from './model.ts';
 type Snapshot = NonNullable<Parameters<ReturnType<typeof MSAModelF>['create']>[0]>;
 export declare function installSvgTestEnv(contextExtras?: Partial<CanvasRenderingContext2D>): void;
-export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
+export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?: number): import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("./types.ts").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -18,7 +19,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -412,6 +413,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
@@ -453,6 +456,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawTree(arg: boolean): void;
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: import("./types.ts").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
@@ -489,7 +493,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     minimapHeight: number;
     marginLeft: number;
     error: unknown;
-    warnings: string[];
+    loadWarnings: string[];
+    dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
@@ -504,7 +509,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHeight(height: number): void;
     setError(error?: unknown): void;
     addWarning(warning: string): void;
-    clearWarnings(): void;
     setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
@@ -521,6 +525,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setColWidth(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: import("./types.ts").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -567,6 +574,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
+    readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
@@ -579,6 +587,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
         root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
@@ -618,9 +627,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
-    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly treeLayout: {
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
+        leaves: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
     readonly totalHeight: number;
-    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
     readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
@@ -646,7 +660,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly labelWidthScale: number;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
     readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
@@ -660,6 +673,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     globalColToVisibleCol(globalCol: number): number | undefined;
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
     visibleSpan({ row, start: rawStart, end: rawEnd }: import("./types.ts").Region): {
         startCol: number;
@@ -692,19 +706,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
-    readonly maxScrollX: number;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
     readonly maxScrollY: number;
     readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
     setScrollZoom(arg: boolean): void;
     setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -730,8 +751,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         onCancel?: () => void;
     }): void;
 } & {
-    readonly verticalScrollbarWidth: 0 | 20;
-    readonly msaCanvasWidth: number;
     cellAt(visibleCol: number, rowIndex?: number): import("./types.ts").Cell;
     readonly hoveredCell: import("./types.ts").Cell | undefined;
     readonly clickedCell: import("./types.ts").Cell | undefined;
@@ -772,6 +791,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
     readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
     readonly tipLabelColors: Map<string, string> | undefined;
@@ -784,18 +823,20 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     zoomToRegion(region: import("./types.ts").Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
-} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeWidth"> & {
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("./types.ts").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -807,7 +848,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1201,6 +1242,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    treeRoot: import("@jbrowse/mobx-state-tree").IType<import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined, import("./types.ts").TreeRoot | undefined>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
@@ -1242,6 +1285,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setDrawTree(arg: boolean): void;
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
+    setTreeOrder(order: import("./types.ts").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
@@ -1278,7 +1322,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     minimapHeight: number;
     marginLeft: number;
     error: unknown;
-    warnings: string[];
+    loadWarnings: string[];
+    dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
@@ -1293,7 +1338,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setHeight(height: number): void;
     setError(error?: unknown): void;
     addWarning(warning: string): void;
-    clearWarnings(): void;
     setHostCarriesData(arg: boolean): void;
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
@@ -1310,6 +1354,9 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setColWidth(n: number): void;
     setCurrentAlignment(n: number): void;
     toggleCollapsed(node: string): void;
+    toggleRotated(node: string): void;
+    clearRotated(): void;
+    setTreeRoot(treeRoot?: import("./types.ts").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
         msa?: string;
@@ -1356,6 +1403,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
+    readonly inputTree: import("./types.ts").NodeWithIds;
     readonly tree: import("./types.ts").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
@@ -1368,6 +1416,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         letters: string;
     } | undefined;
     readonly root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
+    readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
         root: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
@@ -1407,9 +1456,14 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
-    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>;
+    readonly treeLayout: {
+        root: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>;
+        leaves: import("./hierarchy.ts").LaidOutNode<import("./types.ts").NodeWithIds>[];
+        rootToTipLength: number;
+    };
+    readonly hierarchy: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>;
     readonly totalHeight: number;
-    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIdsAndLength>[];
+    readonly leaves: import("./hierarchy.ts").HierarchyNode<import("./types.ts").NodeWithIds>[];
     readonly rootToTipLength: number;
     readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
@@ -1435,7 +1489,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly labelWidthScale: number;
     readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
     readonly secondaryStructureArcs: import("./types.ts").Arc[] | undefined;
     readonly adapterTrackModels: import("./types.ts").BasicTrack[];
     readonly basePairTrackModels: import("./types.ts").BasicTrack[];
@@ -1449,6 +1502,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     globalColToVisibleCol(globalCol: number): number | undefined;
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqEndToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
     visibleSpan({ row, start: rawStart, end: rawEnd }: import("./types.ts").Region): {
         startCol: number;
@@ -1481,19 +1535,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
+    readonly verticalScrollbarWidth: 0 | 20;
+    readonly msaCanvasWidth: number;
+    readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
-    readonly maxScrollX: number;
+    readonly dataWarnings: string[];
+    readonly warnings: string[];
     readonly maxScrollY: number;
     readonly wheelZoomAxis: import("./constants.ts").ScrollZoomAxis;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    clearWarnings(): void;
     setScrollZoom(arg: boolean): void;
     setScrollZoomAxis(arg: import("./constants.ts").ScrollZoomAxis): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    rerootAt(nodeId: string): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
+    zoomAtCenter(scaleFactor: number, axis?: import("./constants.ts").ScrollZoomAxis): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -1519,8 +1580,6 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         onCancel?: () => void;
     }): void;
 } & {
-    readonly verticalScrollbarWidth: 0 | 20;
-    readonly msaCanvasWidth: number;
     cellAt(visibleCol: number, rowIndex?: number): import("./types.ts").Cell;
     readonly hoveredCell: import("./types.ts").Cell | undefined;
     readonly clickedCell: import("./types.ts").Cell | undefined;
@@ -1561,6 +1620,26 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("./types.ts").ResolvedEncoding[];
+    readonly rowPanelScales: ({
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'strip';
+        field: string;
+        colors: Map<string, string>;
+    } | {
+        header: string;
+        legend: import("./types.ts").LegendEntry[];
+        legendTitle?: string;
+        kind: 'features';
+        x: 'column' | 'position';
+        field?: string;
+        colors: Map<import("msa-parsers").Annotation, {
+            fill: string;
+            stroke: string;
+        }>;
+        labels?: Map<import("msa-parsers").Annotation, string>;
+    })[];
     readonly resolvedRowPanels: import("./types.ts").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
     readonly tipLabelColors: Map<string, string> | undefined;
@@ -1573,6 +1652,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("./renderToSvg.tsx").ExportSvgOptions): Promise<void>;
+    exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
@@ -1589,6 +1669,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1693,6 +1774,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("./types.ts").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
@@ -1721,6 +1804,7 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     treeAreaWidth: number;
     treeWidth: number;
     showBranchLen: boolean;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
@@ -1825,6 +1909,8 @@ export declare function createTestModel(snapshot: Omit<Snapshot, 'type'>, width?
     } | undefined;
     currentAlignment: number;
     collapsed: string[];
+    rotated: string[];
+    treeRoot: import("./types.ts").TreeRoot | undefined;
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;

package/dist/types.d.ts

@@ -269,10 +269,27 @@ export interface Highlight {
 /**
  * What the viewer draws over a clade. `highlight` fills the rows behind it,
  * across the tree and the alignment. `bracket` draws a bar and the clade's
- * `label` in the gutter right of the tip labels. `collapse` and `focus` seed
- * the collapsed list and the subtree in focus at load.
+ * `label` in the gutter right of the tip labels. `collapse`, `focus` and
+ * `rotate` seed the collapsed list, the subtree in focus and the rotated nodes
+ * at load.
  */
-export type CladeMark = 'highlight' | 'bracket' | 'collapse' | 'focus';
+export type CladeMark = 'highlight' | 'bracket' | 'collapse' | 'focus' | 'rotate';
+/**
+ * The order each node's children draw in, top to bottom. `branchLength` puts
+ * the shortest branch first, `input` keeps the file's order, `ladderize` puts
+ * the clade with the fewest tips first, so the deep clades step down toward
+ * the bottom, and `ladderizeReverse` puts the one with the most tips first.
+ */
+export type TreeOrder = 'branchLength' | 'input' | 'ladderize' | 'ladderizeReverse';
+/**
+ * Where the tree is rooted: `midpoint` halfway along the longest path between
+ * two tips, and `{outgroup}` on the branch above those tips' most recent common
+ * ancestor, or above the rest of the tips' where the outgroup straddles the
+ * root the file gives.
+ */
+export type TreeRoot = 'midpoint' | {
+    outgroup: string[];
+};
 /**
  * A clade of the tree and the mark drawn over it. `mrca` names tips whose most
  * recent common ancestor is the clade; `range` names the first and last tip of
@@ -316,8 +333,9 @@ export interface Region {
 /**
  * A cell of the alignment in the host's coordinates, 1-based like Highlight:
  * `column` counts every column of the file, hidden gappy ones included, and
- * `residue` counts the row's own letters, absent on a gap. A pointer over a
- * track has a column and no row.
+ * `residue` counts the row's own letters, absent on a gap. `letter` is the
+ * character in the cell, the gap character (`-` or `.`) on a gap. A pointer
+ * over a track has a column and no row.
  */
 export interface Cell {
     column: number;
@@ -369,10 +387,5 @@ export interface NodeWithIds {
     length?: number;
     noTree?: boolean;
 }
-export interface NodeWithIdsAndLength {
-    id: string;
-    name: string;
-    children: NodeWithIdsAndLength[];
-    noTree?: boolean;
-    length: number;
-}
+/** @deprecated the same type as `NodeWithIds` */
+export type NodeWithIdsAndLength = NodeWithIds;

package/dist/useMsaSvgFigure.d.ts

@@ -8,7 +8,8 @@ export interface MsaSvgFigure {
 /**
  * The viewer's SVG export of its viewport, as markup for the page to insert.
  * It redraws after the view settles: `delay` ms after the last scroll, zoom,
- * resize or change to the snapshot. A draw a later one overtakes is dropped.
+ * resize, highlight or change to the snapshot. A draw a later one overtakes is
+ * dropped.
  *
  * The figure's row names and letters are SVG text, so the browser's find
  * locates them, a reader can select them, and print stylesheets apply.