react-msaview 9.0.0 → 9.1.1

package/dist/model.d.ts

@@ -2,13 +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';
-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'>;
 /**
  * The snapshot properties reset() carries across a return to the import form:
  * display preferences and layout, nothing derived from the loaded file.
@@ -22,6 +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
  *
@@ -49,17 +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]>;
@@ -67,7 +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
@@ -77,6 +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
@@ -105,6 +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
@@ -557,10 +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]>;
     /**
@@ -602,9 +616,10 @@ 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>;
     /**
@@ -647,11 +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;
-    setOverviewHeight(n: number): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -664,12 +679,33 @@ 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
      * 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
      */
@@ -682,6 +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
      */
@@ -815,6 +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
@@ -904,6 +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
@@ -1012,23 +1069,11 @@ 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
-     * 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.
@@ -1124,6 +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
      */
@@ -1258,7 +1313,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * any band size.
      */
     readonly treeOverviewLayout: {
-        root: HierarchyNode<NodeWithIds>;
+        root: import("./hierarchy.ts").LaidOutNode<NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -1340,11 +1395,17 @@ 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>;
     /**
@@ -1385,6 +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).
@@ -1437,12 +1506,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * the tree's own units
      */
     readonly rootToTipLength: number;
-    /**
-     * #getter
-     * x-position of the farthest tip in a phylogram, px: effectiveTreeWidth,
-     * 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
@@ -1688,8 +1751,9 @@ 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;
@@ -1720,7 +1784,24 @@ 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[]>;
 } & {
     /**
@@ -1761,6 +1842,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #getter
      */
     readonly blocks2d: (readonly [number, number])[];
+    /**
+     * #getter
+     */
+    readonly wheelZooming: boolean;
     /**
      * #getter
      */
@@ -1831,7 +1916,9 @@ 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;
     /**
@@ -1844,22 +1931,6 @@ 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
      */
@@ -1880,6 +1951,17 @@ 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
      */
@@ -1898,13 +1980,6 @@ 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
@@ -1943,6 +2018,13 @@ 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
      */
@@ -2043,9 +2125,9 @@ 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.
      */
@@ -2226,6 +2308,14 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      */
     setHideHeader(arg: boolean): void;
+    /**
+     * #action
+     */
+    setEmbeddedMode(arg: boolean): void;
+    /**
+     * #action
+     */
+    setImportForm(arg: boolean): void;
     /**
      * #action
      * focus the subtree a click `y` pixels down the tree overview lands on.
@@ -2256,8 +2346,8 @@ 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;
     /**
@@ -2267,7 +2357,7 @@ 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
@@ -2275,6 +2365,14 @@ 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,
@@ -2298,7 +2396,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #action
      */
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
@@ -2311,21 +2409,24 @@ 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;
@@ -2448,21 +2549,24 @@ 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;