react-msaview 8.4.1 → 9.1.0

package/dist/model/treeModel.d.ts

@@ -14,15 +14,18 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
-     * width of the area the tree is drawn in, px
+     * width of the area the tree and its labels draw in, px. Undefined fits
+     * the area to the labels and the tree; `effectiveTreeAreaWidth` reads
+     * the width either way
      */
-    treeAreaWidth: 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>>;
     /**
      * #property
-     * width of the tree within the treeArea, px. automatically synced to
-     * fit within treeAreaWidth
+     * width of the tree within the tree area, px. Undefined gives the tree
+     * the area less the labels; `effectiveTreeWidth` reads the width either
+     * way
      */
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     /**
      * #property
      * use "branch length" e.g. evolutionary distance to draw tree branch
@@ -64,24 +67,19 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * height of the tree overview band, px
      */
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    /**
-     * #property
-     * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
-     * instead of using a fixed width. useful when there is no tree, so the
-     * label gutter isn't padded out to the default 400px
-     */
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     /**
      * #action
-     * set tree area width (px)
+     * set the tree area width, px, or undefined to fit it to the labels and
+     * the tree. The tree then fills the area less the labels
      */
-    setTreeAreaWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
     /**
      * #action
-     * set tree width (px)
+     * set the tree width, px, or undefined to fill the tree area less the
+     * labels
      */
-    setTreeWidth(n: number): void;
+    setTreeWidth(n: number | undefined): void;
     /**
      * #action
      */
@@ -90,10 +88,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setDrawTree(arg: boolean): void;
-    /**
-     * #action
-     */
-    setAutoTreeAreaWidth(arg: boolean): void;
     /**
      * #action
      */
@@ -114,11 +108,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setShowTreeOverview(arg: boolean): void;
-    /**
-     * #action
-     * set the height of the tree overview band (px)
-     */
-    setOverviewHeight(n: number): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultTreeAreaWidth, defaultTreeWidth, treeOrders, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -18,15 +18,18 @@ export function TreeModelF() {
         labelsAlignRight: stripDefault(types.boolean, defaultLabelsAlignRight),
         /**
          * #property
-         * width of the area the tree is drawn in, px
+         * width of the area the tree and its labels draw in, px. Undefined fits
+         * the area to the labels and the tree; `effectiveTreeAreaWidth` reads
+         * the width either way
          */
-        treeAreaWidth: stripDefault(types.number, defaultTreeAreaWidth),
+        treeAreaWidth: types.maybe(types.number),
         /**
          * #property
-         * width of the tree within the treeArea, px. automatically synced to
-         * fit within treeAreaWidth
+         * width of the tree within the tree area, px. Undefined gives the tree
+         * the area less the labels; `effectiveTreeWidth` reads the width either
+         * way
          */
-        treeWidth: stripDefault(types.number, defaultTreeWidth),
+        treeWidth: types.maybe(types.number),
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
@@ -68,28 +71,24 @@ export function TreeModelF() {
          * height of the tree overview band, px
          */
         overviewHeight: stripDefault(types.number, defaultOverviewHeight),
-        /**
-         * #property
-         * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
-         * instead of using a fixed width. useful when there is no tree, so the
-         * label gutter isn't padded out to the default 400px
-         */
-        autoTreeAreaWidth: stripDefault(types.boolean, false),
     })
         .actions(self => ({
         /**
          * #action
-         * set tree area width (px)
+         * set the tree area width, px, or undefined to fit it to the labels and
+         * the tree. The tree then fills the area less the labels
          */
         setTreeAreaWidth(n) {
-            self.treeAreaWidth = Math.round(n);
+            self.treeAreaWidth = n === undefined ? undefined : Math.round(n);
+            self.treeWidth = undefined;
         },
         /**
          * #action
-         * set tree width (px)
+         * set the tree width, px, or undefined to fill the tree area less the
+         * labels
          */
         setTreeWidth(n) {
-            self.treeWidth = Math.round(n);
+            self.treeWidth = n === undefined ? undefined : Math.round(n);
         },
         /**
          * #action
@@ -103,12 +102,6 @@ export function TreeModelF() {
         setDrawTree(arg) {
             self.drawTree = arg;
         },
-        /**
-         * #action
-         */
-        setAutoTreeAreaWidth(arg) {
-            self.autoTreeAreaWidth = arg;
-        },
         /**
          * #action
          */
@@ -139,13 +132,6 @@ export function TreeModelF() {
         setShowTreeOverview(arg) {
             self.showTreeOverview = arg;
         },
-        /**
-         * #action
-         * set the height of the tree overview band (px)
-         */
-        setOverviewHeight(n) {
-            self.overviewHeight = Math.round(n);
-        },
         /**
          * #action
          */

package/dist/model/treeModel.js.map

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package/dist/model.d.ts

@@ -5,7 +5,6 @@ import type { ExportSvgOptions } from './renderToSvg.tsx';
 import type { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Feature, Highlight, Legend, MsaSelection, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedHighlight, ResolvedSelection, TreeOrder, TreeRoot, ResolvedRowPanel, ResolvedStripPanel, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-import type { InterProScanResults } from 'msa-parsers';
 export declare const defaultTrackHeights: Partial<Record<TrackKind, number>>;
 type StripPanelScale = Omit<ResolvedStripPanel, 'id' | 'width' | 'offsetX'>;
 type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' | 'spans'>;
@@ -49,11 +48,11 @@ export declare const preservedOnReset: Set<string>;
  */
 declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     maxInlineSnapshotBytes?: number;
-}): 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").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<TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -61,7 +60,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     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]>;
@@ -603,9 +601,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #property
      * where the view opens, in `highlights` coordinates: `{row, start,
-     * end}` zooms onto residues of that row, `{start, end}` onto alignment
-     * columns. Applied once the alignment and any tree file have loaded,
-     * then cleared, so a reloaded session keeps the reader's own scroll.
+     * end}` zooms onto residues of that row and scrolls the row to the
+     * middle, `{start, end}` zooms onto alignment columns. Applied once the
+     * alignment and any tree file have loaded, then cleared, so a reloaded
+     * session keeps the reader's own scroll.
      */
     region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
     /**
@@ -643,17 +642,15 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     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: 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;
@@ -672,6 +669,12 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * of the snapshot so a link opened in the full app shows the toolbar.
      */
     hideHeader: boolean;
+    /**
+     * #volatile
+     * shows the import form while the view has no data. MSAViewer turns it
+     * off, since its host supplies the data and the form is the demo app's
+     */
+    importForm: boolean;
     /**
      * #volatile
      */
@@ -1014,13 +1017,11 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
 } & {
     /**
      * #getter
-     * hideGaps takes effect when there are collapsed rows or allowedGappyness < 100
+     * hideGaps takes effect when a collapse or a focus hides rows, whose
+     * residues leave columns all gaps among the rest, or when
+     * allowedGappyness is under 100
      */
     readonly hideGapsEffective: boolean;
-    /**
-     * #getter
-     */
-    readonly realAllowedGappyness: number;
     /**
      * #getter
      * the annotations the overlay, the legend and the encodings draw: the
@@ -1105,10 +1106,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * the row table: extra fields per row, keyed by row name, which the
      * `encodings` channels read. It is stored as the JSON string
      * `data.treeMetadata`, the name that travels in existing links, so the
-     * inline size limit and `treeMetadataFilehandle` cover it. labelWidthMap
-     * reads it on every layout, so a malformed user-supplied file returns {}
-     * instead of throwing out of rendering, and every field is a string by
-     * the time a scale sorts it.
+     * inline size limit and `treeMetadataFilehandle` cover it. The tree area
+     * fit reads it on every layout, so a malformed user-supplied file
+     * returns {} instead of throwing out of rendering, and every field is a
+     * string by the time a scale sorts it.
      */
     readonly rowData: Record<string, Record<string, string> | undefined>;
     /**
@@ -1168,6 +1169,60 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * where no clade draws a bar or a label.
      */
     readonly cladeGutterWidth: number;
+    /**
+     * #getter
+     * whether a tree draws beside the labels: false for a file with no
+     * tree, and with drawTree off
+     */
+    readonly treeDrawn: boolean;
+    /**
+     * #getter
+     * the leaf names of the whole tree and its depth in levels. The fit
+     * reads these, so a collapse or a focus leaves the tree area as it is
+     */
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    /**
+     * #getter
+     * the widest tip label at labelFitFontSize, measured whether or not a
+     * zoom hides the labels
+     */
+    readonly maxTipLabelWidth: number;
+    /**
+     * #getter
+     * the px the tip labels take across the tree area: the widest label at
+     * labelFitFontSize and the gaps either side of it, or 0 with drawLabels
+     * off
+     */
+    readonly labelColumnWidth: number;
+    /**
+     * #getter
+     * the tree area width while treeAreaWidth is undefined: the label column
+     * beside a tree that widens with its depth, up to maxTreeAreaShare of the
+     * view, or the room the row panels leave where there is no alignment.
+     * Where that binds, the tree keeps minTreeWidth and the renderer
+     * ellipsizes the labels
+     */
+    readonly fittedTreeAreaWidth: number;
+    /**
+     * #getter
+     * the width of the area the tree and its labels draw in, px:
+     * treeAreaWidth where set, the fit otherwise
+     */
+    readonly effectiveTreeAreaWidth: number;
+    /**
+     * #getter
+     * the width of the tree, px: treeWidth where set, otherwise the tree
+     * area less the label column, which a zoom hiding the labels gives to
+     * the tree
+     */
+    readonly effectiveTreeWidth: number;
+    /**
+     * #getter
+     */
+    readonly showTreeText: boolean;
     /**
      * #getter
      */
@@ -1206,7 +1261,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * any band size.
      */
     readonly treeOverviewLayout: {
-        root: HierarchyNode<NodeWithIds>;
+        root: import("./hierarchy.ts").LaidOutNode<NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -1288,11 +1343,17 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * lazily per row and cached on the parse.
      */
     seqPosIndex(rowName: string): Int32Array | undefined;
+    /**
+     * #method
+     * the row's aligned sequence by the name the tree gives it, including
+     * rows a collapsed clade hides. `MSA.getRow` resolves a FASTA name whose
+     * colon a Newick tool wrote as an underscore, which `rowMap` does not
+     */
+    rowSequence(name: string): string | undefined;
     /**
      * #getter
-     * every sequence in the alignment, keyed by row name, including rows a
-     * collapsed clade hides. `rows` holds only the rows on screen; lookups
-     * by row name use this
+     * every sequence in the alignment, keyed by the alignment's own row
+     * names, including rows a collapsed clade hides
      */
     readonly rowMap: Map<string, string>;
     /**
@@ -1357,9 +1418,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #getter
      * `root` laid out on new nodes in row and branch-length units, read in
-     * pixels through `rowHeight` and `treeWidth`. A zoom leaves it and every
-     * node in it as they are, and an observer reading a node's `x` or `len`
-     * observes the size it scales by.
+     * pixels through `rowHeight` and `effectiveTreeWidth`. A zoom leaves it
+     * and every node in it as they are, and an observer reading a node's `x`
+     * or `len` observes the size it scales by.
      */
     readonly treeLayout: {
         root: import("./hierarchy.ts").LaidOutNode<NodeWithIds>;
@@ -1385,12 +1446,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * the tree's own units
      */
     readonly rootToTipLength: number;
-    /**
-     * #getter
-     * x-position of the farthest tip in a phylogram, px: treeWidth, or 0 for
-     * a tree with no branch lengths (drawn as a cladogram)
-     */
-    readonly maxBranchLength: number;
     /**
      * #getter
      * pixels per unit of branch length in the phylogram layout, 0 in
@@ -1421,10 +1476,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #getter
      */
     readonly showMsaLetters: boolean;
-    /**
-     * #getter
-     */
-    readonly showTreeText: boolean;
 } & {
     /**
      * #getter
@@ -1456,17 +1507,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      */
     readonly columnTrackModels: BasicTrack[];
 } & {
-    /**
-     * #getter
-     */
-    readonly labelWidthMap: Map<string, number>;
-    /**
-     * #getter
-     * factor turning a labelWidthMap entry into its width at the current
-     * font size
-     */
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
     /**
      * #getter
      */
@@ -1794,7 +1834,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      * swap in a different tree over the same alignment. Clears `collapsed`,
      * `rotated` and `showOnly`, since path-derived node ids (node-0-0-1) from the old
-     * tree would match unrelated nodes in the new one.
+     * tree would match unrelated nodes in the new one, and the tree's
+     * filehandle, which the snapshot would otherwise reopen in place of
+     * the new tree
      */
     replaceTree(newick: string): void;
     /**
@@ -1807,22 +1849,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * zoom by `scaleFactor` about the center of the alignment area
      */
     zoomAtCenter(scaleFactor: number, axis?: ScrollZoomAxis): void;
-    /**
-     * #action
-     */
-    zoomOutHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInVertical(): void;
-    /**
-     * #action
-     */
-    zoomOutVertical(): void;
     /**
      * #action
      */
@@ -1861,13 +1887,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * GFF and must keep a hidden overlay hidden.
      */
     setAnnotations(annotations: Annotation[]): void;
-    /**
-     * #action
-     * set the overlay from raw InterProScan results keyed by row name. Kept
-     * for downstream plugins that hold the EBI wire format; new code should
-     * adapt to Annotation[] and call setAnnotations.
-     */
-    setDomains(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     /**
      * #action
@@ -2189,6 +2208,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     setHideHeader(arg: boolean): void;
+    /**
+     * #action
+     */
+    setImportForm(arg: boolean): void;
     /**
      * #action
      * focus the subtree a click `y` pixels down the tree overview lands on.
@@ -2238,6 +2261,14 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * its width, or for a span that resolves to no visible column.
      */
     zoomToRegion(region: Region): void;
+    /**
+     * #action
+     * zoomToRegion, and for a region naming a row, also scroll that row to
+     * the middle of the alignment, as Go to does. What `region` opens on; a
+     * caller following a range as it moves wants zoomToRegion alone, which
+     * leaves the reader's vertical scroll where they put it.
+     */
+    revealRegion(region: Region): void;
     /**
      * #action
      * zoom and scroll so the selected columns fill the alignment's width,
@@ -2271,8 +2302,8 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: TreeOrder;
     drawTree: boolean;
@@ -2280,7 +2311,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks: ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
@@ -2409,8 +2439,8 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: TreeOrder;
     drawTree: boolean;
@@ -2418,7 +2448,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;