react-msaview 6.5.0 → 7.0.0

package/dist/model.d.ts

@@ -1,6 +1,6 @@
 import type { HierarchyNode } from './hierarchy.ts';
 import type { ExportSvgOptions } from './renderToSvg.tsx';
-import type { Annotation, BasicTrack, ColumnTrackSpec, DomainBand, Highlight, NodeWithIds, NodeWithIdsAndLength, ResolvedHighlight } from './types.ts';
+import type { Annotation, Arc, BasicTrack, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Highlight, NodeWithIds, NodeWithIdsAndLength, ResidueMapping, ResolvedHighlight, RowResidue, StructureResidue, UnshareableData } 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';
@@ -55,7 +55,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     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" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     /**
      * #property
      * id of view, randomly generated if not provided
@@ -548,6 +548,15 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * text track. See docs/layers.md
      */
     columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>>, [undefined]>;
+    /**
+     * #property
+     * which residue of which structure each row's residues are, as data.
+     * The viewer cannot infer this -- matching a row to a structure by
+     * sequence equality fails for a tagged construct, a truncation or a
+     * subsequence row, and fails in the direction that looks like it
+     * worked -- so it arrives computed. See docs/layers.md
+     */
+    residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ResidueMapping, ResidueMapping, ResidueMapping>>, [undefined]>;
     /**
      * #property
      * data from the loaded tree/msa/treeMetadata, generally loaded by
@@ -568,8 +577,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>, [undefined]>;
     /**
      * #property
+     * the user's explicit hide choices per annotation accession, keyed by
+     * accession with the value meaning "off", the same shape as
+     * `turnedOffTracks`. An accession the user has never touched is absent
+     * and drawn, so a file of two hundred domain types adds nothing to the
+     * shared URL until someone filters one out
      */
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     /**
      * #property
      */
@@ -623,7 +637,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     /**
@@ -688,6 +701,15 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * array of column indices to highlight
      */
     highlightedColumns: number[] | undefined;
+    /**
+     * #volatile
+     * transient highlights keyed by who asked for them. One slot cannot hold
+     * two sources -- a structure viewer's hover and a genome view's hover
+     * both want to point at a column, and with one slot whoever clears last
+     * erases the other's. Keyed by owner, each source adds and removes only
+     * its own. Not persisted: a hover is not part of the document.
+     */
+    transientHighlights: Record<string, Highlight[]>;
     /**
      * #volatile
      */
@@ -696,6 +718,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #volatile
      */
     conservationTrackHeight: number;
+    /**
+     * #volatile
+     * heights of individual `columnTracks`, by track id. A data track is
+     * resized on its own: the shared per-kind heights below belong to the
+     * tracks the viewer computes, and dragging a data track's handle used to
+     * resize those instead.
+     */
+    columnTrackHeights: Record<string, number>;
     /**
      * #volatile
      * taller than the conservation track by default: the logo spends its
@@ -703,6 +733,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * one too short to identify
      */
     sequenceLogoTrackHeight: number;
+    /**
+     * #volatile
+     */
+    arcTrackHeight: number;
     /**
      * #volatile
      */
@@ -711,6 +745,29 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #volatile
      */
     error: unknown;
+    /**
+     * #volatile
+     * load problems the view carried on through: an optional layer that did
+     * not arrive, an overlay that did not parse. `error` is the other kind --
+     * it replaces the view, which is right for the alignment and wrong for a
+     * decorative file
+     */
+    warnings: string[];
+    /**
+     * #volatile
+     * bumped by reset(). The React error boundary above the view keeps its
+     * caught error until it is remounted, so "Return to import form" did
+     * nothing after a render error until this became its key
+     */
+    resetCount: number;
+    /**
+     * #volatile
+     * set by a host that restores the loaded documents by its own means --
+     * a jbrowse session that holds them, a page that refetches them on load.
+     * `unshareableData` then reports nothing, since what it warns about is a
+     * link that opens empty, and under such a host the link does not
+     */
+    hostCarriesData: boolean;
     /**
      * #volatile
      * overlay annotations drawn on the alignment, whatever their source.
@@ -763,28 +820,57 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * set error state
      */
     setError(error?: unknown): void;
+    /**
+     * #action
+     * report something the view survived: a layer that failed to load, a
+     * file that failed to parse
+     */
+    addWarning(warning: string): void;
+    /**
+     * #action
+     */
+    clearWarnings(): void;
+    /**
+     * #action
+     * declare that this host restores the loaded documents itself, which
+     * takes down the "Not in the link" warning. See `hostCarriesData`
+     */
+    setHostCarriesData(arg: boolean): void;
     /**
      * #action
      * set mouse position (row, column) in the MSA
      *
-     * CROSS-REPO CONTRACT: jbrowse-plugin-protein3d calls this (and reads the
-     * `mouseCol` volatile) to sync MSA<->3D-structure hover. Keep the name and
-     * signature stable; see that repo's ProteinToMsaHoverSync.tsx.
+     * PUBLIC API: a host drives this (and reads the `mouseCol` volatile) to
+     * sync the alignment's hover with a view of its own -- a genome view, a
+     * 3D structure. Keep the name and signature stable.
      */
     setMousePos(col?: number, row?: number): void;
     /**
      * #action
      * set highlighted columns
      *
-     * CROSS-REPO CONTRACT: called by jbrowse-plugin-msaview
-     * (afterCreateAutoruns.ts) to highlight alignment columns. It has no
-     * in-repo caller, so do not flag it as dead code — it is public API.
+     * PUBLIC API: jbrowse-plugin-msaview calls this from its
+     * afterCreateAutoruns to highlight alignment columns, and MSAViewer
+     * passes its `highlightColumns` prop through it. Not dead code.
      */
     setHighlightedColumns(columns?: number[]): void;
     /**
      * #action
      */
     setHighlights(highlights: Highlight[]): void;
+    /**
+     * #action
+     * show `highlights` on behalf of `owner`, replacing whatever that owner
+     * showed before and leaving every other owner's alone. The object is
+     * replaced rather than mutated so one assignment is the observable
+     * change.
+     */
+    applyHighlight(owner: string, highlights: Highlight[]): void;
+    /**
+     * #action
+     * drop what `owner` was showing, leaving every other owner's in place
+     */
+    clearHighlight(owner: string): void;
     /**
      * #action
      * toggle the annotation overlay on the alignment
@@ -816,7 +902,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setColWidth(n: number): void;
     /**
      * #action
-     *
+     * switch to another alignment of a multi-alignment file (Stockholm). The
+     * new alignment has its own rows and its own tree, so everything naming
+     * the old one's -- the collapsed node ids, the subtree in focus, the
+     * reference row, the scroll position -- goes with it
      */
     setCurrentAlignment(n: number): void;
     /**
@@ -869,6 +958,15 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setTreeMetadata(result: string): void;
+    /**
+     * #action
+     * keep the GFF text the way the alignment and the tree are kept, rather
+     * than only its parsed annotations. The annotations are volatile, so a
+     * file opened from disk used to leave no trace in the snapshot at all --
+     * not the text, and not the filehandle, which is cleared once a blob is
+     * read. An autorun parses this back into annotations.
+     */
+    setGFF(result: string): void;
 } & {
     /**
      * #getter
@@ -883,17 +981,26 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly actuallyShowDomains: boolean;
+    /**
+     * #getter
+     * whether this host brings the loaded documents back by means the
+     * snapshot cannot see, which is what decides whether `unshareableData`
+     * has anything to warn about.
+     *
+     * A simple host flips the `hostCarriesData` volatile. A host whose
+     * answer depends on how the view was opened overrides this getter in a
+     * `.views` block of its own composed model -- jbrowse-plugin-msaview's
+     * indexed-location views refetch from a URL the session holds, while its
+     * data-store views really are absent from a link someone pastes
+     * elsewhere. `unshareableData` reads it off `self`, so an override wins.
+     */
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     /**
      * #getter
      */
     readonly width: number;
 } & {
-    /**
-     * #method
-     * unused here, but can be used by derived classes to add extra items
-     */
-    extraViewMenuItems(): never[];
     /**
      * #getter
      */
@@ -922,6 +1029,25 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    /**
+     * #getter
+     * the loaded documents this view's own snapshot cannot carry, largest
+     * first. A file opened from disk or pasted in becomes inline text, and
+     * DataModel drops an inline document past `maxInlineSnapshotBytes`
+     * rather than put megabytes of sequence into a session or a URL.
+     *
+     * Dropping it is right. Dropping it silently is what makes a copied link
+     * open an empty viewer, so the header says so and the standalone app
+     * stops rewriting the address bar while this is non-empty. A document
+     * fetched from a URL never appears here whatever its size: the snapshot
+     * keeps the filehandle and refetches through it.
+     *
+     * Nothing is unshareable when the host restores the data by its own
+     * means (see `hostRestoresData`) -- inside a session that reloads these
+     * documents from somewhere the snapshot does not show, the warning is
+     * simply wrong.
+     */
+    readonly unshareableData: UnshareableData[];
     menuItems(): never[];
     /**
      * #getter
@@ -1005,14 +1131,22 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     readonly numRows: number;
     /**
-     * #getter
-     * per-row index of the global column holding each ungapped sequence
-     * position, so seqPos -> column is a lookup rather than a scan of the row.
-     * The domain overlay resolves thousands of these per redraw.
+     * #method
+     * index of the global column holding each ungapped sequence position of a
+     * row, so seqPos -> column is a lookup rather than a scan. The domain
+     * overlay resolves thousands of these per redraw.
+     *
+     * Built per row, on the row asked for: the first lookup used to index
+     * every row in the alignment. The cache is keyed on the parse the rows
+     * came from, so a new alignment brings a new one.
      */
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     /**
      * #getter
+     * every sequence the alignment holds, keyed by row name, whatever the
+     * tree currently shows. `rows` is the rows on screen; this is the rows
+     * that exist, and every lookup about a named row goes through it --
+     * collapsing a clade hides rows, it does not delete their sequence
      */
     readonly rowMap: Map<string, string>;
     /**
@@ -1089,9 +1223,25 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     readonly leaves: HierarchyNode<NodeWithIdsAndLength>[];
     /**
      * #getter
-     * max branch length across the tree, used to scale phylogram x-positions
+     * branch-length extent of the displayed tree, root to farthest tip, in
+     * the tree's own units
+     */
+    readonly rootToTipLength: number;
+    /**
+     * #getter
+     * x-position of the farthest tip in a phylogram, px. The layout scales
+     * the longest root-to-tip path onto treeWidth, so that is where it lands
+     * -- and 0 for a tree carrying no lengths at all, which draws as a
+     * cladogram instead
      */
     readonly maxBranchLength: number;
+    /**
+     * #getter
+     * pixels per unit of branch length in the current phylogram layout, and 0
+     * in cladogram mode, where the x-positions carry no length at all. The
+     * scale bar over the tree is drawn from it.
+     */
+    readonly pxPerBranchLength: number;
     /**
      * #getter
      * max topological depth to a tip, used to scale cladogram x-positions
@@ -1112,43 +1262,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     readonly totalWidth: number;
 } & {
-    /**
-     * #getter
-     */
-    readonly dataInitialized: boolean;
-    /**
-     * #getter
-     */
-    readonly blocksX: number[];
-    /**
-     * #getter
-     */
-    readonly blocksY: number[];
-    /**
-     * #getter
-     * height of the alignment viewport, px. The same subtraction as
-     * msaAreaHeight, which is defined later in the views chain
-     */
-    readonly visibleMsaHeight: number;
-} & {
-    /**
-     * #getter
-     */
-    readonly blocks2d: (readonly [number, number])[];
-    /**
-     * #getter
-     */
-    readonly isLoading: boolean;
-    /**
-     * #getter
-     */
-    readonly maxScrollX: number;
-    /**
-     * #getter
-     * most-negative allowed scrollY, keeping the last row in view rather than
-     * letting the whole alignment scroll off the top.
-     */
-    readonly maxScrollY: number;
     /**
      * #getter
      */
@@ -1157,113 +1270,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly showTreeText: boolean;
-} & {
-    /**
-     * #action
-     */
-    setDrawMsaLetters(arg: boolean): void;
-    /**
-     * #action
-     */
-    setScrollZoom(arg: boolean): void;
-    /**
-     * #action
-     * set hovered tree node and its descendants
-     */
-    setHoveredTreeNode(nodeId?: string): void;
-    /**
-     * #action
-     * Calculate a neighbor joining tree from the current MSA using BLOSUM62 distances
-     */
-    calculateNeighborJoiningTreeFromMSA(): void;
-    /**
-     * #action
-     * restore the default column width and row height
-     */
-    resetZoom(): void;
-    /**
-     * #action
-     */
-    zoomOutHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInHorizontal(): void;
-    /**
-     * #action
-     */
-    zoomInVertical(): void;
-    /**
-     * #action
-     */
-    zoomOutVertical(): void;
-    /**
-     * #action
-     */
-    zoomIn(): void;
-    /**
-     * #action
-     */
-    zoomOut(): void;
-    /**
-     * #action
-     * Smoothly zoom by a continuous scaleFactor. The column under the cursor
-     * (offsetX/offsetY, px relative to the MSA area) stays anchored
-     * horizontally. Vertically the anchor is biased toward the top: when the
-     * alignment nearly fits the viewport, snap to y=0 rather than pinning a
-     * random row under the cursor, with the bias fading out as the alignment
-     * grows taller than the viewport (where cursor-anchoring is useful).
-     * Drives wheel/trackpad-pinch zoom.
-     */
-    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
-    /**
-     * #action
-     */
-    doScrollY(deltaY: number): void;
-    /**
-     * #action
-     * set scroll Y-offset (px), clamped to keep the alignment in view
-     */
-    setScrollY(n: number): void;
-    /**
-     * #action
-     * Set the overlay annotations and reveal the overlay in a single step (an
-     * empty list clears both). Every source funnels through here after its
-     * own adapter has flattened it: InterProScan, GFF, user uploads, NCBI CDD.
-     */
-    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
-     */
-    doScrollX(deltaX: number): void;
-    /**
-     * #action
-     */
-    setScrollX(n: number): void;
-    /**
-     * #action
-     */
-    setColumnTracks(tracks: ColumnTrackSpec[]): void;
-    /**
-     * #action
-     */
-    toggleTrack(id: string): void;
-    /**
-     * #action
-     */
-    setStatus(status?: {
-        msg: string;
-        url?: string;
-        onCancel?: () => void;
-    }): void;
 } & {
     /**
      * #getter
@@ -1284,6 +1290,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly seqConsensus: string | undefined;
+    /**
+     * #getter
+     * the base pairs of the consensus secondary structure, as arcs. The WUSS
+     * string is collapsed through the hidden columns before it is parsed, so
+     * the pairs land in the same visible column space the text track does
+     */
+    readonly secondaryStructureArcs: Arc[] | undefined;
     /**
      * #getter
      */
@@ -1296,6 +1309,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     readonly columnTrackContent: Map<string, {
         values?: number[];
         data?: string;
+        arcs?: Arc[];
     }>;
     /**
      * #getter
@@ -1304,6 +1318,20 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
+    /**
+     * #getter
+     * the consensus secondary structure as a track, when there is one. Its
+     * own getter so the object keeps its identity across a zoom: the canvas
+     * redraws on the track it is handed changing, and rebuilding these
+     * alongside everything else made every zoom frame redraw every track
+     */
+    readonly basePairTrackModels: BasicTrack[];
+    /**
+     * #getter
+     * the tracks computed from the alignment itself, which depend on their
+     * own heights and on the alphabet -- and on nothing zoom changes
+     */
+    readonly computedTrackModels: BasicTrack[];
     readonly tracks: BasicTrack[];
     /**
      * #getter
@@ -1327,10 +1355,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Convert a visible column to a row-specific sequence position (0-based).
      * Returns undefined if the position is a gap in the sequence.
      *
-     * CROSS-REPO CONTRACT: this and the sibling coordinate converters
-     * (seqPosToVisibleCol, globalColToVisibleCol, seqPosToGlobalCol) are used
-     * by jbrowse-plugin-protein3d to translate between alignment columns and
-     * structure/sequence residue positions across gaps. Keep them stable.
+     * PUBLIC API: this and the sibling coordinate converters
+     * (visibleColToGlobalCol, seqPosToVisibleCol, globalColToVisibleCol,
+     * seqPosToGlobalCol) are how a host translates between alignment columns
+     * and a row's residue positions across gaps. Keep them stable.
      *
      * @param rowName - The name of the row
      * @param visibleCol - The visible column index
@@ -1357,15 +1385,28 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * @returns The visible column index, or undefined if the column is hidden
      */
     globalColToVisibleCol(globalCol: number): number | undefined;
+    /**
+     * #method
+     * Convert a visible column index (what a mouse handler reports) back to a
+     * column of the full alignment. Hidden columns shift everything to their
+     * right, so a host that holds per-column data of its own has to make this
+     * hop before indexing it.
+     *
+     * @param visibleCol - The visible column index
+     * @returns The global column index in the full MSA
+     */
+    visibleColToGlobalCol(visibleCol: number): number;
     /**
      * #method
      * Convert a sequence position (ungapped) to a global column index.
+     * Returns undefined for a row the alignment does not have -- answering
+     * anyway is how a mistyped or stale row name came to highlight column 0.
      *
      * @param rowName - The name of the row
      * @param seqPos - The sequence position (0-based, ungapped)
-     * @returns The global column index in the full MSA
+     * @returns The global column index in the full MSA, or undefined
      */
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
     /**
      * #method
      * Convert a sequence position (ungapped) directly to a visible column index.
@@ -1376,10 +1417,73 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * @returns The visible column index, or undefined if the column is hidden
      */
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    /**
+     * #getter
+     * every reason a mapping is being ignored, so a host can say which. A
+     * mapping outlives the alignment it was computed for; when the two no
+     * longer agree the lookups have to refuse, and refusing invisibly is how
+     * "there is no structure here" gets confused with "this data is stale".
+     */
+    readonly residueMappingProblems: ResidueMappingProblem[];
+    /**
+     * #getter
+     * the mappings that still fit the loaded alignment. A row-level problem
+     * takes the whole mapping out; a single malformed segment takes only
+     * itself, since the rest of the mapping is still a claim about residues
+     * that exist.
+     */
+    readonly usableResidueMappings: ResidueMapping[];
+    /**
+     * #getter
+     * the structures the loaded alignment has usable mappings onto. A row can
+     * have several -- an experimental entry and a predicted model, say -- so
+     * a host that means a particular one has to name it.
+     */
+    readonly mappedStructures: {
+        row: string;
+        structure: import("./types.ts").MappedStructure;
+    }[];
+    /**
+     * #method
+     * The structure residue a row residue is, or undefined. Refusing is the
+     * point: the guess this replaces answered every query, with a wrong
+     * residue when it did not know.
+     *
+     * It also refuses when the answer is not unique. A row commonly maps onto
+     * several structures -- an experimental entry and two predicted models --
+     * and returning whichever came first would be the same class of wrong,
+     * quieter. Name one with `structureId`, or use `mappedStructures` to see
+     * what there is.
+     *
+     * Positions are 1-based, as `residueMappings` and `highlights` are --
+     * note that the column helpers above take 0-based ones.
+     *
+     * @param rowName - The alignment row
+     * @param seqPos - Residue of that row, 1-based
+     * @param structureId - Which structure, when the row maps onto several
+     */
+    structureResidue(rowName: string, seqPos: number, structureId?: string): StructureResidue | undefined;
+    /**
+     * #method
+     * The row residue a structure residue is, the same lookup backwards, and
+     * refusing on the same terms. `asymId` picks between mappings onto the
+     * same entry, which a homodimer -- two rows, two chains, one id -- always
+     * needs; without it such a lookup is ambiguous and gets nothing.
+     *
+     * @param structureId - The structure's id, as the mapping names it
+     * @param position - Residue of that structure, 1-based label_seq_id
+     * @param asymId - Which chain, when the id alone is ambiguous
+     */
+    rowResidue(structureId: string, position: number, asymId?: string): RowResidue | undefined;
 } & {
     /**
      * #getter
-     * widget width minus the tree area gives the space for the MSA
+     * the vertical space the alignment rows actually get: the widget height
+     * less everything stacked above and below them -- the header, the tracks,
+     * and the minimap when the columns overflow. Every consumer wants this
+     * same subtraction, so there is one of it: blocksY, maxScrollY, the
+     * vertical scrollbar and fitVertically all read it, and a second getter
+     * that forgot the tracks is what put the last rows out of reach.
      */
     readonly msaAreaHeight: number;
     /**
@@ -1399,6 +1503,165 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly showVerticalScrollbar: boolean;
+} & {
+    /**
+     * #getter
+     */
+    readonly dataInitialized: boolean;
+    /**
+     * #getter
+     */
+    readonly blocksX: number[];
+    /**
+     * #getter
+     */
+    readonly blocksY: number[];
+} & {
+    /**
+     * #getter
+     */
+    readonly blocks2d: (readonly [number, number])[];
+    /**
+     * #getter
+     */
+    readonly isLoading: boolean;
+    /**
+     * #getter
+     */
+    readonly maxScrollX: number;
+    /**
+     * #getter
+     * most-negative allowed scrollY, keeping the last row in view rather than
+     * letting the whole alignment scroll off the top.
+     */
+    readonly maxScrollY: number;
+} & {
+    /**
+     * #action
+     */
+    setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     */
+    setScrollZoom(arg: boolean): void;
+    /**
+     * #action
+     * set hovered tree node and its descendants
+     */
+    setHoveredTreeNode(nodeId?: string): void;
+    /**
+     * #action
+     * Calculate a neighbor joining tree from the current MSA using BLOSUM62
+     * distances. Refuses above `maxNeighborJoiningRows`: the join loop is
+     * cubic and runs on the main thread, so 800 rows is a ten-second freeze
+     * with no progress and no cancel, and a tree that size wants a tool built
+     * for it anyway.
+     */
+    calculateNeighborJoiningTreeFromMSA(): void;
+    /**
+     * #action
+     * swap in a different tree over the same alignment. Node ids are derived
+     * from the path (node-0-0-1), so a `collapsed` or `showOnly` id held over
+     * from the old tree matches a real node in the new one and folds whatever
+     * happens to sit there -- the ids go with the tree they name.
+     */
+    replaceTree(newick: string): void;
+    /**
+     * #action
+     * restore the default column width and row height
+     */
+    resetZoom(): void;
+    /**
+     * #action
+     */
+    zoomOutHorizontal(): void;
+    /**
+     * #action
+     */
+    zoomInHorizontal(): void;
+    /**
+     * #action
+     */
+    zoomInVertical(): void;
+    /**
+     * #action
+     */
+    zoomOutVertical(): void;
+    /**
+     * #action
+     */
+    zoomIn(): void;
+    /**
+     * #action
+     */
+    zoomOut(): void;
+    /**
+     * #action
+     * Smoothly zoom by a continuous scaleFactor. The column under the cursor
+     * (offsetX/offsetY, px relative to the MSA area) stays anchored
+     * horizontally. Vertically the anchor is biased toward the top: when the
+     * alignment nearly fits the viewport, snap to y=0 rather than pinning a
+     * random row under the cursor, with the bias fading out as the alignment
+     * grows taller than the viewport (where cursor-anchoring is useful).
+     * Drives wheel/trackpad-pinch zoom.
+     */
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    /**
+     * #action
+     */
+    doScrollY(deltaY: number): void;
+    /**
+     * #action
+     * set scroll Y-offset (px), clamped to keep the alignment in view
+     */
+    setScrollY(n: number): void;
+    /**
+     * #action
+     * Set the overlay annotations (an empty list clears them). Every source
+     * funnels through here after its own adapter has flattened it:
+     * InterProScan, GFF, user uploads, NCBI CDD.
+     *
+     * It does not touch `showDomains`. Loading used to force the overlay on,
+     * and since a restored snapshot loads its GFF again on the way in, a link
+     * shared with the overlay hidden reopened with it drawn.
+     */
+    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
+     */
+    doScrollX(deltaX: number): void;
+    /**
+     * #action
+     */
+    setScrollX(n: number): void;
+    /**
+     * #action
+     */
+    setColumnTracks(tracks: ColumnTrackSpec[]): void;
+    /**
+     * #action
+     * replace the alignment<->structure correspondence (see docs/layers.md)
+     */
+    setResidueMappings(mappings: ResidueMapping[]): void;
+    /**
+     * #action
+     */
+    toggleTrack(id: string): void;
+    /**
+     * #action
+     */
+    setStatus(status?: {
+        msg: string;
+        onCancel?: () => void;
+    }): void;
 } & {
     /**
      * #getter
@@ -1536,10 +1799,18 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setConservationTrackHeight(arg: number): void;
+    /**
+     * #action
+     */
+    setColumnTrackHeight(id: string, height: number): void;
     /**
      * #action
      */
     setSequenceLogoTrackHeight(arg: number): void;
+    /**
+     * #action
+     */
+    setArcTrackHeight(arg: number): void;
     /**
      * #action
      * Return to the import form: every property off `preservedOnReset`
@@ -1552,8 +1823,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     exportSVG(opts: ExportSvgOptions): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    /**
+     * #action
+     * draw this annotation type, or stop drawing it. Only the "stop" is
+     * recorded -- see `turnedOffFeatures`
+     */
+    setFilter(accession: string, shown: boolean): void;
     /**
      * #action
      */
@@ -1679,7 +1954,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: Highlight[];
@@ -1801,7 +2077,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: Highlight[];