react-msaview 9.1.0 → 9.2.0

package/dist/index.js

@@ -21,6 +21,8 @@ export { default as MSAView } from './components/Loading.js';
 export { default as MSAViewer } from './components/MSAViewer.js';
 // the snapshot MSAViewer builds from its props, for the CLI's --props
 export { resolveTheme, viewerSnapshot } from './viewerSnapshot.js';
+// the active scheme's hex color for a row residue, to paint a structure with
+export { schemeResidueColor } from './schemeResidueColor.js';
 export { mount } from './mount.js';
 export { defineMsaElement } from './element.js';
 export { useMsaSvgFigure } from './useMsaSvgFigure.js';

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,6EAA6E;AAC7E,+DAA+D;AAC/D,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,mEAAmE;AACnE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAA;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAA;AACzD,4EAA4E;AAC5E,mCAAmC;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AACvD,6EAA6E;AAC7E,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAA;AAO1D,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAE7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AAEjE,sEAAsE;AACtE,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAClE,6EAA6E;AAC7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAC5D,OAAO,EAAE,KAAK,EAAE,MAAM,YAAa,CAAA;AACnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAGtD,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model/treeModel.d.ts

@@ -62,6 +62,11 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * subtree boxed. A click on it focuses the subtree under the pointer
      */
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draw the branch-length scale bar above the tree of a phylogram
+     */
+    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * height of the tree overview band, px
@@ -108,6 +113,10 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setShowTreeOverview(arg: boolean): void;
+    /**
+     * #action
+     */
+    setShowTreeScaleBar(arg: boolean): 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, treeOrders, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultShowTreeScaleBar, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -66,6 +66,11 @@ export function TreeModelF() {
          * subtree boxed. A click on it focuses the subtree under the pointer
          */
         showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
+        /**
+         * #property
+         * draw the branch-length scale bar above the tree of a phylogram
+         */
+        showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
         /**
          * #property
          * height of the tree overview band, px
@@ -132,6 +137,12 @@ export function TreeModelF() {
         setShowTreeOverview(arg) {
             self.showTreeOverview = arg;
         },
+        /**
+         * #action
+         */
+        setShowTreeScaleBar(arg) {
+            self.showTreeScaleBar = arg;
+        },
         /**
          * #action
          */

package/dist/model/treeModel.js.map

@@ -1 +1 @@
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package/dist/model.d.ts

@@ -2,12 +2,11 @@ import type { ColumnStats } from './columnStats.ts';
 import type { ScrollZoomAxis } from './constants.ts';
 import type { HierarchyNode } from './hierarchy.ts';
 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 { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Feature, Highlight, Legend, MsaSelection, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedStripPanel, ResolvedHighlight, ResolvedSelection, TreeRoot, ResolvedRowPanel, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
+import type { ZoomSnapshot } from './zoomSnapshot.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 export declare const defaultTrackHeights: Partial<Record<TrackKind, number>>;
-type StripPanelScale = Omit<ResolvedStripPanel, 'id' | 'width' | 'offsetX'>;
-type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' | 'spans'>;
 /**
  * The snapshot properties reset() carries across a return to the import form:
  * display preferences and layout, nothing derived from the loaded file.
@@ -21,6 +20,8 @@ type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' |
  * Exported for modelReset.test.ts.
  */
 export declare const preservedOnReset: Set<string>;
+type StripPanelScale = Omit<ResolvedStripPanel, 'id' | 'width' | 'offsetX'>;
+type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' | 'spans'>;
 /**
  * #stateModel MsaView
  *
@@ -48,17 +49,18 @@ export declare const preservedOnReset: Set<string>;
  */
 declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     maxInlineSnapshotBytes?: number;
-}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     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]>;
+    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]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -66,7 +68,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     /**
      * #property
      * id of view, randomly generated if not provided
@@ -76,6 +78,13 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #property
      */
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * whether shown domains fill the cells they cover. Off, the residue
+     * scheme keeps the cells and each domain draws as a bar under its
+     * row. See `cellFill`.
+     */
+    domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * whether the domain legend is expanded. The legend floats over the
@@ -104,6 +113,12 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #property
      */
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draws the toolbar's menus and Settings as icons without text, for a
+     * host with little room, such as a JBrowse view
+     */
+    embeddedMode: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * zoom in/out on plain mouse-wheel without holding ctrl
@@ -556,10 +571,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     }>, [undefined]>;
     /**
      * #property
-     * the user's explicit hide choices per annotation accession, keyed by
-     * accession with the value meaning "off", like `turnedOffTracks`. An
-     * untouched accession is absent and drawn, so the shared URL grows
-     * only with the user's filters
+     * the user's departures from each annotation accession's default,
+     * keyed by accession with the value meaning "off", like
+     * `turnedOffTracks`. An untouched accession is absent and takes its
+     * default, so the shared URL grows only with the user's filters
      */
     turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     /**
@@ -647,10 +662,11 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     setLabelsAlignRight(arg: boolean): void;
     setDrawTree(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
-    setTreeOrder(order: TreeOrder): void;
+    setTreeOrder(order: import("./types.ts").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -663,6 +679,21 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #volatile
      */
     headerHeight: number;
+    /**
+     * #volatile
+     * whether the settings panel docks beside the alignment, taking
+     * `settingsPanelWidth` out of the width the view lays out in
+     */
+    settingsOpen: boolean;
+    /**
+     * #volatile
+     * the log scale a wheel zoom has gathered against the detent at the
+     * default column width and row height, per axis
+     */
+    zoomHeld: {
+        col: number;
+        row: number;
+    };
     /**
      * #volatile
      * leaves the toolbar out, for a host drawing its own controls. Kept out
@@ -687,6 +718,13 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * canvas scale factor, from the device pixel ratio
      */
     highResScaleFactor: number;
+    /**
+     * #volatile
+     * the cell size and block grid the alignment last drew at, held from a
+     * wheel-zoom frame until the gesture settles. MSACanvas stretches those
+     * blocks to the current cell size with one CSS transform
+     */
+    zoomSnapshot: ZoomSnapshot | undefined;
     /**
      * #volatile
      */
@@ -820,6 +858,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     setWidth(arg: number): void;
+    /**
+     * #action
+     */
+    setSettingsOpen(arg: boolean): void;
     /**
      * #action
      * update the canvas scale factor when the device pixel ratio changes
@@ -909,6 +951,16 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * toggle the annotation overlay on the alignment
      */
     setShowDomains(arg: boolean): void;
+    /**
+     * #action
+     */
+    setDomainFill(arg: boolean): void;
+    /**
+     * #action
+     * hand the cell fill to the residue scheme, the domains, or neither,
+     * which colors the letters instead
+     */
+    setCellFill(mode: 'residue' | 'domain' | 'none'): void;
     /**
      * #action
      * expand or collapse the domain legend that floats over the alignment
@@ -1022,16 +1074,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * allowedGappyness is under 100
      */
     readonly hideGapsEffective: boolean;
-    /**
-     * #getter
-     * the annotations the overlay, the legend and the encodings draw: the
-     * GFF's, then the `features` layer's
-     */
-    readonly allAnnotations: Annotation[];
-    /**
-     * #getter
-     */
-    readonly actuallyShowDomains: boolean;
     /**
      * #getter
      * whether the host restores the loaded documents outside the snapshot.
@@ -1127,6 +1169,16 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #getter
      */
     readonly MSA: import("msa-parsers").MSAParserType | null;
+    /**
+     * #getter
+     * the annotations the overlay, the legend and the encodings draw: the
+     * GFF's, the `features` layer's, then the file's own per-row lines
+     */
+    readonly allAnnotations: Annotation[];
+    /**
+     * #getter
+     */
+    readonly actuallyShowDomains: boolean;
     /**
      * #getter
      */
@@ -1394,6 +1446,14 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * ref http://www.jalview.org/help/html/colourSchemes/clustal.html
      */
     readonly colClustalX: Record<string, string>[];
+    /**
+     * #getter
+     * Pre-computed similarity shades per column, for blosum62_dynamic.
+     * Returns a map of letter -> color for each column. Amino acids shade by
+     * BLOSUM62 similarity to the rest of the column, and an alignment of
+     * nucleotides by identity, since the matrix names amino acids.
+     */
+    readonly colSimilarity: Record<string, string>[];
     /**
      * #getter
      * Conservation score per column using Shannon entropy (biojs-msa style).
@@ -1534,6 +1594,12 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * and the alphabet, not on zoom
      */
     readonly computedTrackModels: BasicTrack[];
+    /**
+     * #getter
+     * the reference row (`relativeTo`) repeated above the alignment, so it
+     * stays in view while the rows compared against it scroll
+     */
+    readonly referenceTrackModels: BasicTrack[];
     readonly tracks: BasicTrack[];
     /**
      * #getter
@@ -1691,8 +1757,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
 } & {
     /**
      * #getter
-     * the branch-length scale bar over the tree, undefined in cladogram mode
-     * or when the tree area is too narrow for one
+     * the branch-length scale bar over the tree, undefined while
+     * `showTreeScaleBar` is off, in cladogram mode, or when the tree area is
+     * too narrow for one
      */
     readonly treeScaleBar: {
         step: number;
@@ -1723,7 +1790,24 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * filter dialog and the palettes
      */
     readonly annotationTypes: Map<string, Annotation>;
+    /**
+     * accessions hidden until the user turns them on, such as a Stockholm
+     * file's #=GR lines
+     */
+    readonly defaultOffAccessions: Set<string>;
+    /**
+     * #method
+     */
+    featureOff(accession: string): boolean;
     readonly filteredAnnotations: Annotation[];
+    /**
+     * #getter
+     * what colors the alignment's cells: the residue scheme, the domains
+     * covering them, or nothing, which leaves the scheme to the letters.
+     * Domains own the fill only while some are drawn, so a file whose
+     * annotations all start hidden keeps its residue colors
+     */
+    readonly cellFill: 'residue' | 'domain' | 'none';
     readonly annotationsByRow: Record<string, Annotation[]>;
 } & {
     /**
@@ -1764,6 +1848,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #getter
      */
     readonly blocks2d: (readonly [number, number])[];
+    /**
+     * #getter
+     */
+    readonly wheelZooming: boolean;
     /**
      * #getter
      */
@@ -1869,6 +1957,17 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * other one can change how much of the alignment fits.
      */
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: ScrollZoomAxis): void;
+    /**
+     * #action
+     * zoomToPos for one wheel or pinch frame. The alignment keeps the blocks
+     * it drew at the start of the gesture, scaled, and redraws them only once
+     * they stop covering the viewport; endWheelZoom redraws them sharp
+     */
+    wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    /**
+     * #action
+     */
+    endWheelZoom(): void;
     /**
      * #action
      */
@@ -1925,6 +2024,13 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     toggleTrack(id: string): void;
+    /**
+     * #action
+     * show or hide several tracks at once, as the track selector's Show all
+     * and Hide all do. A choice matching the track's default is dropped, so
+     * it stays out of the shared URL
+     */
+    setTracksShown(ids: string[], shown: boolean): void;
     /**
      * #action
      */
@@ -2025,9 +2131,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #getter
      * whether the overlay marks each domain with a bar under its row instead
-     * of filling the row behind the letters. Letter-color mode hands the
-     * background to the color scheme, so a filled box would paint over it and
-     * leave the setting with nothing to show. Sub-row layout already stacks
+     * of filling the row behind the letters: whenever the domains do not own
+     * the cell fill (`cellFill`), a filled box would paint over the residue
+     * colors the user picked. Sub-row layout already stacks
      * the boxes clear of the letters, and with the letters too small to draw
      * the filled box is the only thing left to read.
      */
@@ -2208,6 +2314,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     setHideHeader(arg: boolean): void;
+    /**
+     * #action
+     */
+    setEmbeddedMode(arg: boolean): void;
     /**
      * #action
      */
@@ -2242,8 +2352,8 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     exportNewick(): void;
     /**
      * #action
-     * show or hide an annotation type. Only hidden types are recorded; see
-     * `turnedOffFeatures`
+     * show or hide an annotation type. Only a choice that differs from the
+     * type's default is recorded; see `turnedOffFeatures`
      */
     setFilter(accession: string, shown: boolean): void;
     /**
@@ -2253,7 +2363,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #action
      */
-    fitVertically(): void;
+    fitVertically(maxRowHeight?: any): void;
     /**
      * #action
      * zoom and scroll so a span fills the alignment's width, in highlight
@@ -2292,7 +2402,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #action
      */
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
@@ -2305,21 +2415,24 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     treeAreaWidth: number | undefined;
     treeWidth: number | undefined;
     showBranchLen: boolean;
-    treeOrder: TreeOrder;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks: ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
@@ -2442,21 +2555,24 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     treeAreaWidth: number | undefined;
     treeWidth: number | undefined;
     showBranchLen: boolean;
-    treeOrder: TreeOrder;
+    treeOrder: import("./types.ts").TreeOrder;
     drawTree: boolean;
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;